Microbiome based systems, apparatus and methods for the exploration and production of hydrocarbons

ABSTRACT

There are provided methods, systems and processes for the utilization of microbial and related genetic information for use in the exploration, determination, production and recovery of natural resources, including energy sources, and the monitoring, control and analysis of processes and activities.

This application: (i) claims, under 35 U.S.C. § 119(e)(1), the benefitof the filing date of Dec. 31, 2013 of U.S. provisional application Ser.No. 61/922,734; and (ii) claims, under 35 U.S.C. § 119(e)(1), thebenefit of the filing date of Feb. 26, 2014 of U.S. provisionalapplication Ser. No. 61/944,961; and is a continuation-in-part of U.S.patent application Ser. No. 14/585,078 filed Dec. 29, 2014, the entiredisclosures of each of which are incorporated herein by reference.

This invention was made with Government support under SBIR award number1416179 by the National Science Foundation. The Government has certainrights in this invention.

REFERENCE TO AN ELECTRONIC SEQUENCE LISTING

The content of the electronic sequence listing (B2a_ST25.txt; Size 13KB; and Date of Creation Jun. 20, 2015) is herein incorporated byreference in its entirety.

BACKGROUND OF THE INVENTION Field of the Invention

The present inventions relate to novel and unique apparatus, systems,and methods for monitoring, analyzing, planning and controlling theexploration and production of natural resources, including energyresources, such, as geothermal and hydrocarbons. There has been acontinuous need for a better understanding of the factors and conditionsthat influence and relate to the exploration and production ofhydrocarbons, such as natural gas and oil. Thus, great efforts have beenmade in areas such as geologic evaluation, seismic, pressure sensing,radiation, sonic, logging while drilling, (“LWD”), measuring whiledrilling (“MWD”), and combinations thereof MWD/LWD, which efforts havealmost exclusively focused on traditional sensing, analysis and controlmethodologies.

The art of exploring and producing hydrocarbons, however, has largelyignored the microbial and genetic information that is present in, orassociated with, hydrocarbon exploration and production including suchinformation that is associated with a borehole, borehole fluids,borehole cuttings, a formation, a reservoir, a pay zone and an oilfield. While efforts have been made to evaluate a particular microbialpresent in an oil or natural gas well, these efforts have largelyfocused on identification of a particular microbe, e.g., through DNAanalysis, for the purposes of eliminating undesirable microbes andincreasing beneficial ones. Further, analysis and work has taken placeto genetically engineer microbes to meet, or fulfill, a particularfunction in hydrocarbon production and clean up. However, it is believedthat prior to the present inventions, the use of microbial and geneticinformation, has never been used, and was not able to be used, for thepurposes of monitoring, analyzing, planning and controlling theexploration and production of hydrocarbons.

Thus, and in general, the present inventions provide apparatus, systemsand methods for determining and characterizing the microbiome associatedwith hydrocarbon exploration and production, obtaining such microbiomeinformation, converting such information into a form that is useful inthe exploration and production of hydrocarbons, and using suchinformation in the exploration and production of hydrocarbons, andcombinations and variations of these. In view of the ubiquitous natureof genetic material and microorganisms, the present inventions provide,among other things, the ability to control, enhance, plan, monitor, andpredict performance of, hydrocarbon exploration and productionactivities.

The terms microbiome, microbiome information; microbiome data, andsimilar such terms are used herein in the broadest possible sense,unless expressly stated otherwise, and would include: a census ofcurrently present microorganisms, both living and nonliving, which mayhave been present months, years, millennia or longer (“the microbiota”);a census of components of the microbiome other than bacteria andarchaea, e.g., viruses and microbial eukaryotes; population studies andcharacterizations of microorganisms, genetic material, and biologicmaterial; a census of any detectable biological material; andinformation that is derived or ascertained from genetic material,biomolecular makeup, fragments of genetic material, DNA, RNA, protein,carbohydrate, metabolite profile, fragment of biological materials andcombinations and variations of these.

As used herein, the terms historic microbiome information and historicmicrobiome data are to be given their broadest possible meaning, unlessspecified otherwise, and includes publicly available databases, e.g.,the Earth Microbiome Project, the Human Microbiome Project, AmericanGut, GreenGenes, the Ribosomal Database Project, the InternationalNucleotide Sequence Database Collaboration (INSDC), American Gut, etc.,regarding the microbiome. It would also include databases that are basedupon real-time microbiome data and derived microbiome data. Thesedatabases may be cloud-based, locally-based, or hosted on remote systemsother than cloud-based systems.

As used herein, the terms real-time microbiome information and real-timemicrobiome data are to be given their broadest possible meaning, unlessspecified otherwise, and includes microbiome information that iscollected or obtained at a particular industrial setting during anindustrial activity, which would include for example sampling anddetermining the microbiome present in a pipeline flow, in returns fromdrilling a borehole, in hydraulic fracturing fluid, agricultural runoffor soil samples taken during a planting or harvesting.

As used herein, the terms derived microbiome information and derivedmicrobiome data are to be given their broadest possible meaning, unlessspecified otherwise, and includes any real-time, historic, andcombinations of these, microbiome information that has beencomputationally linked or used to create a relationship such as forexample evaluating the microbiome of hydraulic fracturing fluid before,during, and after hydraulic fracturing stages, evaluating the microbiomebetween planting and harvesting, and evaluating the historic microbiomeof deep core samples with the microbiome of hydrocarbon productdelivered from the well. Thus, derived microbiome information providesinformation about the industrial process setting or activity that maynot be readily ascertained from non-derived information.

As used herein, the terms predictive microbiome information andpredictive microbiome data are to be given their broadest possiblemeaning, unless specified otherwise, and includes information that isbased upon combinations and computational links or processing ofhistoric, predictive, real-time, and derived microbiome information,data, and combinations, variations and derivatives of these, whichinformation predicts, forecasts, directs, or anticipates a futureoccurrence, event, state, or condition in the industrial setting, orallows interpretation of a current or past occurrence. Thus, by way ofexample, predictive microbiome information would include: adetermination and comparison of real-time microbiome information and thederived microbiome information of an exploratory process to identify ahydrocarbon source; a comparison of real-time microbiome informationcollected during the advancement of a borehole to predict a perforationor hydraulic fracturing pattern; a determination and comparison ofderived microbiome information and historic microbiome information of achemical processing plant to identify an enhanced efficiency in theprocess; and, a comparison and analysis of historic microbiome datafrom, for example, core samples and derived microbiome information fromwell cutting returns to characterize a formation.

Real-time, derived, and predicted data may be collected and stored, andthus, become historic data for an ongoing or future process, setting, orapplication.

As used herein, unless specified otherwise, the terms “hydrocarbonexploration and production”, “exploration and production activities”,“E&P”, and “E&P activities”, and similar such terms are to be giventheir broadest possible meaning, and include surveying, geologicalanalysis, well planning, reservoir planning, reservoir management,drilling a well, workover and completion activities, hydrocarbonproduction, flowing of hydrocarbons from a well, collection ofhydrocarbons, secondary and tertiary recovery from a well, themanagement of flowing hydrocarbons from a well, and any other upstreamactivities.

As used herein, unless specified otherwise, the term “earth” should begiven its broadest possible meaning, and includes, the ground, allnatural materials, such as rocks; and artificial materials, such asconcrete, that are or may be found in the ground.

As used herein, unless specified otherwise “offshore” and “offshoredrilling activities” and similar such terms are used in their broadestsense and would include drilling activities on, or in, any body ofwater, whether fresh or salt water, whether manmade or naturallyoccurring, such as for example rivers, lakes, canals, inland seas,oceans, seas, such as the North Sea, bays and gulfs, such as the Gulf ofMexico. As used herein, unless specified otherwise the term “offshoredrilling rig” is to be given its broadest possible meaning and wouldinclude fixed towers, tenders, platforms, barges, jack-ups, floatingplatforms, drill ships, dynamically positioned drill ships,semi-submersibles and dynamically positioned semi-submersibles. As usedherein, unless specified otherwise the term “seafloor” is to be givenits broadest possible meaning and would include any surface of the earththat lies under, or is at the bottom of, any body of water, whetherfresh or salt water, whether manmade or naturally occurring.

As used herein, unless specified otherwise, the term “borehole” shouldbe given it broadest possible meaning and includes any opening that iscreated in the earth that is substantially longer than it is wide, suchas a well, a well bore, a well hole, a micro hole, a slimhole and otherterms commonly used or known in the arts to define these types of narrowlong passages. Wells would further include exploratory, production,abandoned, reentered, reworked, and injection wells. They would includeboth cased and uncased wells, and sections of those wells. Uncasedwells, or section of wells, also are called open holes, or open holesections. Boreholes may further have segments or sections that havedifferent orientations, they may have straight sections and arcuatesections and combinations thereof. Thus, as used herein unless expresslyprovided otherwise, the “bottom” of a borehole, the “bottom surface” ofthe borehole and similar terms refer to the end of the borehole, i.e.,that portion of the borehole furthest along the path of the boreholefrom the borehole's opening, the surface of the earth, or the borehole'sbeginning. The terms “side” and “wall” of a borehole should to be giventheir broadest possible meaning and include the longitudinal surfaces ofthe borehole, whether or not casing or a liner is present, as such,these terms would include the sides of an open borehole or the sides ofthe casing that has been positioned within a borehole. Boreholes may bemade up of a single passage, multiple passages, connected passages,(e.g., branched configuration, fishboned configuration, or combconfiguration), and combinations and variations thereof.

As used herein, unless specified otherwise, the term “advancing aborehole”, “drilling a well”, and similar such terms should be giventheir broadest possible meaning and include increasing the length of theborehole. Thus, by advancing a borehole, provided the orientation is nothorizontal and is downward, e.g., less than 90°, the depth of theborehole may also be increased.

Boreholes are generally formed and advanced by using mechanical drillingequipment having a rotating drilling tool, e.g., a bit. For example, andin general, when creating a borehole in the earth, a drilling bit isextending to and into the earth and rotated to create a hole in theearth. To perform the drilling operation the bit must be forced againstthe material to be removed with a sufficient force to exceed the shearstrength, compressive strength or combinations thereof, of thatmaterial. The material that is cut from the earth is generally known ascuttings, e.g.: waste, which may be chips of rock, dust, rock fibers andother types of materials and structures that may be created by the bit'sinteractions with the earth. These cuttings are typically removed fromthe borehole by the use of fluids, which fluids can be liquids, foams orgases, or other materials know to the art.

The true vertical depth (“TVD”) of a borehole is the distance from thetop or surface of the borehole to the depth at which the bottom of theborehole is located, measured along a straight vertical line. Themeasured depth (‘MD’) of a borehole is the distance as measured alongthe actual path of the borehole from the top or surface to the bottom.As used herein unless specified otherwise the term depth of a boreholewill refer to MD. In general, a point of reference may be used for thetop of the borehole, such as the rotary table, drill floor, well head orinitial opening or surface of the structure in which the borehole isplaced.

As used herein, unless specified otherwise, the term “drill pipe” is tobe given its broadest possible meaning and includes all forms of pipeused for drilling activities; and refers to a single section or piece ofpipe. As used herein the terms “stand of drill pipe,” “drill pipestand,” “stand of pipe,” “stand” and similar type terms should be giventheir broadest possible meaning and include two, three or four sectionsof drill pipe that have been connected, e.g., joined together, typicallyby joints having threaded connections. As used herein the terms “drillstring,” “string,” “string of drill pipe,” string of pipe” and similartype terms should be given their broadest definition and would include astand or stands joined together for the purpose of being employed in aborehole. Thus, a drill string could include many stands and manyhundreds of sections of drill pipe.

As used herein, unless specified otherwise, the terms “blowoutpreventer,” “BOP,” and “BOP stack” should be given their broadestpossible meanings, and include devices positioned at or near theborehole surface, e.g., the surface of the earth including dry land orthe seafloor, which are used to contain or manage pressures or flowsassociated with a borehole and other combinations and assemblies of flowand pressure management devices to control borehole pressures, flows orboth and, in particular, to control or manage emergency flow or pressuresituations.

As used herein, unless specified otherwise, the terms “drill bit”,“bit”, “drilling bit” or similar such terms, should be given theirbroadest possible meaning and include all tools designed or intended tocreate a borehole in an object, a material, a work piece, a surface, theearth or a structure including structures within the earth, and wouldinclude bits used in the oil, gas and geothermal arts, such as fixedcutter and roller cone bits, as well as, other types of bits, such as,rotary shoe, drag-type, fishtail, adamantine, single and multi-toothed,cone, reaming cone, reaming, self-cleaning, disc: three-cone, rollingcutter, crossroller, jet, core, impreg and hammer bits, and combinationsand variations of the these.

As used herein, unless specified otherwise, the terms “workover,”“completion” and “workover and completion” and similar such terms shouldbe given their broadest possible meanings and would include activitiesthat place at or near the completion of drilling a well, activities thattake place at or the near the commencement of production from the well:activities that take place on the well when the well is a producing oroperating well, activities that take place to reopen or reenter anabandoned or plugged well or branch of a well, and would also includefor example, perforating, cementing, acidizing, fracturing, pressuretesting, the removal of well debris, removal of plugs, insertion orreplacement of production tubing, forming windows in casing to drill orcomplete lateral or branch wellbores, cutting and milling operations ingeneral, insertion of screens, stimulating, cleaning, testing, analyzingand other such activities.

As used herein, unless specified otherwise, the terms “formation,”“reservoir,” “pay zone,” and similar terms, are to be given theirbroadest possible meanings and would include all locations, areas, andgeological features within the earth that contain, may contain, or arebelieved to contain, hydrocarbons.

As used herein, unless specified otherwise, the terms “field,” “oilfield” and similar terms, are to be given their broadest possiblemeanings, and would include any area of land, sea floor, or water thatis loosely or directly associated with a formation, and moreparticularly with a resource containing formation, thus, a field mayhave one or more exploratory and producing wells associated with it, afield may have one or more governmental body or private resource leasesassociated with it, and one or more field(s) may be directly associatedwith a resource containing formation.

Drilling and Completing Wells

In the production of natural resources from formations, reservoirs,deposits, or locations within the earth a well or borehole is drilledinto the earth to the location where the natural resource is believed tobe located. These natural resources may be a hydrocarbon reservoir,containing natural gas, crude oil and combinations of these; the naturalresource may be fresh water; it may be a heat source for geothermalenergy; or it may be some other natural resource that is located withinthe ground.

These resource-containing formations may be at or near the surface, ator near the sea floor, a few hundred feet, a few thousand feet, or tensof thousands of feet below the surface of the earth, including under thefloor of a body of water, e.g., below the sea floor. In addition tobeing at various depths within the earth, these formations may coverareas of differing sizes, shapes and volumes.

Unfortunately, and generally, when a well is drilled into theseformations the natural resources rarely flow into the well at rates,durations and amounts that are economically viable. This problem occursfor several reasons, some of which are understood, others of which arenot as well understood, and some of which may not yet be known. Theseproblems can relate to the viscosity of the natural resource, theporosity of the formation, the geology of the formation, the formationpressures, and the openings that place the resource recovery conduit,e.g., production tubing, in the well in fluid communication with theformation, to name a few.

Typically, and by way of general illustration, in drilling a well aninitial borehole is made into the earth, e.g., surface of land orseabed, and then subsequent and smaller diameter boreholes are drilledto extend the overall depth of the borehole. Thus, as the overallborehole gets deeper its diameter becomes smaller; resulting in what canbe envisioned as a telescoping assembly of holes with the largestdiameter hole being at the top of the borehole closest to the surface ofthe earth.

Thus, by way of example, the starting phases of a subsea drill processmay be explained in general as follows. Once the drilling rig ispositioned on the surface of the water over the area where drilling isto take place, an initial borehole is made by drilling a 36″ hole in theearth to a depth of about 200-300 ft. below the seafloor. A 30″ casingis inserted into this initial borehole. This 30″ casing may also becalled a conductor. The 60″ conductor may or may not be cemented intoplace. During this drilling operation a riser is generally not used andthe cuttings from the borehole, e.g., the earth and other materialremoved from the borehole by the drilling activity are returned to theseafloor. Next, a 26″ diameter borehole is drilled within the 30″casing, extending the depth of the borehole to about 1,000-1,500 ft.This drilling operation may also be conducted without using a riser. A20″ casing is then inserted into the 30″ conductor and 26″ borehole.This 20″ casing is cemented into place. The 20″ casing has a wellheadsecured to it. (In other operations an additional smaller diameterborehole may be drilled, and a smaller diameter casing inserted intothat borehole with the wellhead being secured to that smaller diametercasing.) A BOP is then secured to a riser and lowered by the riser tothe sea floor; where the BOP is secured to the wellhead. From this pointforward all drilling activity in the borehole takes place through theriser and the BOP.

For a land based drill process, the steps are similar, although thelarge diameter tubulars, 30″-20″ are typically not used. Thus, andgenerally, there is a surface casing that is typically about 13⅜″diameter. This may extend from the surface, e.g., wellhead and BOP, todepths of tens of feet to hundreds of feet. One of the purposes of thesurface casing is to meet environmental concerns in protecting groundwater. The surface casing should have sufficiently large diameter toallow the drill string, product equipment such as ESPs and circulationmud to pass by. Below the casing one or more different diameterintermediate casings may be used. (It is understood that sections of aborehole may not be cased, which sections are referred to as open hole.)These can have diameters in the range of about 9″ to about 7″, althoughlarger and smaller sizes may be used, and can extend to depths ofthousands and tens of thousands of feet. Inside of the casing andextending from a pay zone, or production zone of the borehole up to andthrough the wellhead on the surface is the production tubing. There maybe a single production tubing or multiple production tubings in a singleborehole, with each of the production tubing endings being at differentdepths.

Typically, when completing a well, it is necessary to perform aperforation operation, and also in some instances perform a hydraulicfracturing, or fracing operation. In general, when a well has beendrilled and casing, e.g., a metal pipe, is run to the prescribed depth,the casing is typically cemented in place by pumping cement down andinto the annular space between the casing and the earth. The casing,among other things, prevents the hole from collapsing and fluids fromflowing between permeable zones in the annulus. (In some situations onlythe metal casing is present, in others there may be two metal casingpresent one inside of the other, there may be more that two metal casingpresent each inside of the other, in still others the metal casing andcement are present, and in others there could be other configurations ofmetal, cement and metal; and in others there may be an open hole, e.g.,no casing, liner or cement is present, at the location of interest inthe borehole.) Thus, this casing forms a structural support for the welland a barrier to the earth.

While important for the structural integrity of the well, the casing andcement present a problem when they are in the production zone. Thus, inaddition to holding back the earth, they also prevent the hydrocarbonsfrom flowing into the well and from being recovered. Additionally, theformation itself may have been damaged by the drilling process, e.g., bythe pressure from the drilling mud, and this damaged area of theformation may form an additional barrier to the flow of hydrocarbonsinto the well. Similarly, in most situations where casing is not neededin the production area, e.g., open hole, the formation itself isgenerally tight, and more typically can be very tight, and thus, willnot permit the hydrocarbons to flow into the well. In some situationsthe formation pressure is large enough that the hydrocarbons readilyflow into the well in an uncased, or open hole. Nevertheless, asformation pressure lessens a point will be reached where the formationitself shuts-off, or significantly reduces, the flow of hydrocarbonsinto the well. Also the low formation pressure could prevent fluid fromflowing from the bottom of the borehole to the surface, requiring theuse of artificial lift.

To overcome this problem of the flow of hydrocarbons into the well beingblocked by the casing, cement and the formation itself, openings, e.g.,perforations, are made in the well in the area of the pay zone.Generally, a perforation is a small, about ¼ to about 1″ or 2″ indiameter hole that extends through the casing, cement and damagedformation and goes into the formation. This hole creates a passage forthe hydrocarbons to flow from the formation into the well. In a typicalwell a large number of these holes are made through the casing and intothe formation in the pay zone.

Generally, in a perforating operation a perforating tool or gun islowered into borehole to the location where the production zone or payzone is located. The perforating gun is a long, typically round tool,that has a small enough diameter to fit into the casing or tubular andreach the area within the borehole where the production zone is believedto be. Once positioned in the production zone a series of explosivecharges, e.g., shaped charges, are ignited. The hot gases and moltenmetal from the explosion cut a hole, i.e., the perf or perforation,through the casing and into the formation. These explosive-madeperforations may only extend a few inches, e.g., 6″ to 18″ into theformation. In hard rock formations the explosive perforation device mayonly extend an inch or so, and may function poorly, if at all.Additionally, because these perforations are made with explosives theytypically have damages areas, which include loose rock and perforationdebris along the bottom of the hole, and a damaged zone extendingannularly around the hole. Beyond the damaged zone is a virgin zoneextending annularly around the damaged zone. The damaged zone, whichtypically encompasses the entire hole, generally, greatly reduces thepermeability of the formation. This has been a long-standing andunsolved problem, among others, with the use of explosive perforations.The perforation holes are made to get through one group of obstructionsto the flow of hydrocarbons into the well, e.g., the casing, and indoing so they create a new group of these obstructions, e.g., thedamaged area encompassing the perforation holes.

The ability of, or ease with which, the natural resource can flow out ofthe formation and into the well or production tubing (into and out of,for example, in the case of engineered geothermal wells, and someadvanced recovery methods for hydrocarbon wells) can generally beunderstood as the fluid communication between the well and theformation. As this fluid communication is increased several enhancementsor benefits may be obtained: the volume or rate of flow (e.g.; gals perminute) can increase; the distance within the formation out from thewell where the natural resources will flow into the well can be increase(e.g., the volume and area of the formation that can be drained by asingle well is increased and it will thus take less total wells torecover the resources from an entire field); the time period when thewell is producing resources can be lengthened; the flow rate can bemaintained at a higher rate for a longer period of time; andcombinations of these and other efficiencies and benefits.

Fluid communication between the formation and the well can be greatlyincreased by the use of hydraulic fracturing techniques. The first usesof hydraulic fracturing date back to the late 1940s and early 1950s. Ingeneral, hydraulic fracturing treatments involve forcing fluids down thewell and into the formation, the fluids enter the formation and crackopen the rock, e.g., force the layers of rock to break apart orfracture. These fractures create channels or flow paths that may havecross sections of a few millimeters, to several millimeters, to severalcentimeters, and potentially larger. The fractures may also extend outfrom the well in all directions for a few feet, several feet and tens offeet or further. It should be remembered that no wellbore or branch of awellbore is perfectly vertical or horizontal. The longitudinal axis ofthe well bore in the reservoir will most likely be on an angle to boththe vertical and the horizontal directions. The borehole could besloping up or down or on occasion be mostly horizontal. The section ofthe well bore located within the reservoir, i.e. the section of theformation containing the natural resources, can be called the pay zone.For example, in the recovery of shale gas and oil the wells aretypically essentially horizontal in the reservoir.

Generally, in a hydraulic fracturing operation a mixture of typically awater based fluid with sand or other small particles, e.g., proppants,is forced into the well and out into the formation (if the well isperforated the fracturing fluid is forced out and through one or more ofthe perforations and into the formation). The fluids used to performhydraulic fracture can range from very simple to multicomponentformulations, e.g., water, water containing gelling agents to increasethe viscosity of the fracturing fluid. Additionally, these fluids, e.g.,tracing fluids or fracturing fluids, typically carry with them proppingagents (proppants). Proppants are small particles, e.g., grains of sandor other material, that are flowed into the fractures and hold open thefractures when the pressure of the fracturing fluid is reduced and thefluid is removed to allow the resource, e.g.; hydrocarbons, to flow intothe well. In this manner the proppants hold open the fractures, keepingthe channels open so that the hydrocarbons can more readily flow intothe well. Additionally, the fractures greatly increase the surface areafrom which the hydrocarbons can flow into the well. Proppants may not beneeded, or generally may not be used when acids are used to create afrac and subsequent channel in a carbonate rich reservoir where theacids dissolve part or all of the rock leaving an opening for theformation fluids to flow to the wellbore.

Typical fluid volumes in a propped fracturing treatment of a formationin general can range from a few thousand to a few million gallons.Proppant volumes can be several thousand cubic feet, and can approachseveral hundred thousand cubic feet. For example, for a single well 3-5million gallons of water may be used and pressures may be in the rangeof about 500 psi and greater, at least about 1,000 psi, about 5,000 psito about 10,000 psi, as high as 15,000 psi and potentially higher. Asthe fracturing fluid and proppants are forced into the formation at highinjection rate, the bottom hole pressure increases enough to overcomethe stresses and the rock tensile strength so that the formations breaksor fractures. Sometimes the breaks occur along planes of weakness thatare called joints. Naturally occurring joints in the formation may alsobe opened, expanded and propagated by the fluid. In order to keep thesenewly formed and enlarged fractures, cracks or joints open, once thepressure and fluid are removed, the proppants are left behind. They inessence hold open, i.e., “prop” open, the newly formed and enlargedfractures, cracks, or joints in the formation.

SUMMARY

Accordingly, there has been a long-standing and unfulfilled need forbetter abilities to monitor, analyze, plan and control the explorationand production of natural resources, and in particular, the explorationand production of hydrocarbon resources. Traditional monitoring andcontrol applications have significant failings and have not fully metthese continuing needs. Accordingly, the present inventions, among otherthings, solve these needs by providing the articles of manufacture,devices and processes taught, disclosed and claimed herein.

Thus, there is provide a method of enhancing the production ofhydrocarbons from a well, the method including: obtaining a firstmicrobiome information at time t₁ from hydrocarbons produced from awell, the well having a first production zone, and a second productionzone; performing an evaluation on the first microbiome information, theevaluation including: a relationship based processing having a relatedgenetic material component and an industrial setting component; and, abioinformatics stage; whereby a microbiome finger print is obtained foreach production zone of the well at time t₁; obtaining a secondmicrobiome information at time t₂ from hydrocarbons produced from thewell; performing an evaluation on the second microbiome information, theevaluation including: a relationship based processing having a relatedgenetic material component and an industrial setting component; and, abioinformatics stage; whereby a second microbiome finger print isobtained for each production zone of the well at time t₂; and, comparingthe first microbiome finger print and the second microbiome fingerprint; whereby any change in the amount of hydrocarbons produced fromeach zone is identified.

Additionally, there is provided the present systems, operations andmethods having one or more of the following features: wherein, the firstmicrobiome information, the second microbiome information, or both thefirst and the second microbiome information are selected from the groupconsisting of historic microbiome information, real time microbiomeinformation, derived microbiome information and predictive microbiomeinformation; wherein, the historic microbiome information is selectedfrom the group consisting of the Earth Microbiome Project, the HumanMicrobiome Project, American Gut, GreenGenes, the Ribosomal DatabaseProject, the International Nucleotide Sequence Database Collaboration(INSDC), and American Gut; wherein, the industrial setting component isselected from the group consisting of GPS data; location data, systemcomponent identification, subsystem component identification, pumpstation true vertical depth of a well, pH, measured depth of a well,processing stage, geological parameter, formation permeability,viscosity, porosity, pressure, flow, and temperature; wherein, thebioinformatics stage includes submitting the microbiome information toQIIME processing; wherein, the bioinformatics stage includes: compilingmetadata mapping; barcode decoding; OTU picking; constructingphylogentic trees; constructing a BIOM table; and UniFac and PCoA;wherein, the bioinformatics stage includes: compiling metadata mapping;barcode decoding; OTU picking; constructing phylogentic trees;constructing a BIOM table; and UniFac and PCoA; wherein, thebioinformatics stage includes: compiling metadata mapping; barcodedecoding; OTU picking; constructing phylogentic trees; constructing aBIOM table; and UniFac and PCoA; wherein, the bioinformatics stageincludes: compiling metadata mapping; OTU picking; constructingphylogentic trees; constructing a BIOM table; and UniFac and PCoA;wherein, the bioinformatics stage includes: compiling metadata mapping;OTU picking; constructing a BIOM table; and UniFac and PCoA; andwherein, the bioinformatics stage includes: constructing a BIOM table;and UniFac and PCoA.

Yet further, there is provided the present systems, operations andmethods having one or more of the following features: wherein a zone inthe well is shut down based at least in part on the comparison (e.g.,comparing the first microbiome finger print and the second microbiomefinger print; whereby any change in the amount of hydrocarbons producedfrom each zone is identified); wherein a zone in the well is shut downbased at least in part on the comparison; wherein a zone in the well isshut down based at least in part on the comparison; wherein a newproduction zone in the well is opened based at least in part on thecomparison; wherein a new production zone in the well is opened based atleast in part on the comparison; and wherein a new production zone inthe well is opened based at least in part on the comparison.

Moreover, there is provided a method of monitoring the production ofhydrocarbons from a well, the method including: obtaining a microbiomeinformation from hydrocarbons produced from a well having a plurality ofproduction zones; and, performing an evaluation on the microbiomeinformation; whereby a microbiome finger print is produced for at leasttwo of the plurality of production zones.

Additionally there is provided the present systems, operations andmethods having one or more of the following features: wherein themicrobiome information comes from a single sample of hydrocarbons;wherein the microbiome information comes from a plurality of samples ofhydrocarbons; wherein the evaluation includes: a relationship basedprocessing having a related genetic material component and an industrialsetting component; and, a bioinformatics stage; wherein, the industrialsetting component is selected from the group consisting of GPS data;location data, system component identification, subsystem componentidentification, pump station true vertical depth of a well, pH, measureddepth of a well, processing stage, geological parameter, formationpermeability, viscosity, porosity, pressure, flow, and temperature;wherein, the bioinformatics stage includes submitting the microbiomeinformation to QIIME processing; and wherein, the bioinformatics stageincludes: compiling metadata mapping; barcode decoding; OTU picking;constructing phylogentic trees; constructing a BIOM table; and UniFacand PCoA.

Further there is provided a method of enhancing the production ofhydrocarbons from an oil field, the method including: obtaining a firstmicrobiome information from hydrocarbons produced from a first well inan oil field having a plurality of wells at time t₁; obtaining a secondmicrobiome information from hydrocarbons produced from a second well inan oil field having a plurality of wells at about time t₂; wherein timet₁ and t₂ can be the same or different day; performing an evaluation onthe first microbiome information, the evaluation including: arelationship based processing having a related genetic materialcomponent and an industrial setting component; and, a bioinformaticsstage; whereby a microbiome finger print is obtained for the first wellat time t₁; performing an evaluation on the second microbiomeinformation, the evaluation including: a relationship based processinghaving a related genetic material component and an industrial settingcomponent; and, a bioinformatics stage; whereby a microbiome fingerprint is obtained for the second well at time t₂; obtaining a secondmicrobiome information from hydrocarbons produced from the first well inthe oil field at time t_(1+n); obtaining a second microbiome informationfrom hydrocarbons produced from the second well in the oil field atabout time t_(2+n); wherein n can be the same or different number ofdays; performing an evaluation on the second microbiome information fromthe first well, the evaluation including: a relationship basedprocessing having a related genetic material component and an industrialsetting component; and, a bioinformatics stage; whereby a microbiomefinger print is obtained for the first well at time t_(1+n); performingan evaluation on the second microbiome information from the second well,the evaluation including: a relationship based processing having arelated genetic material component and an industrial setting component;and, a bioinformatics stage; whereby a microbiome finger print isobtained for the second well at time t_(2+n); and analyzing themicrobiome finger prints and based at least in part on the analysisperforming an activity in the oil field.

Still further there is provided the present systems, operations andmethods having one or more of the following features: wherein theactivity in the oil field includes changing the well spacing for the oilfield; wherein the activity in the oil field includes drilling a newwell; wherein the activity in the oil field includes determining amicrobiome well spacing for the oil field and drilling a new well baseat least in part on the microbiome well spacing; and wherein theactivity in the oil field includes restimulating a well.

Additionally there is provided a method of controlling the production ofhydrocarbons from a well including: analyzing a fluid from a well toprovide a first microbiome information; associating the first microbiomeinformation with an operation condition of the well; obtaining a secondmicrobiome information; associating the second microbiome informationwith the first microbiome information; and, evaluating the firstmicrobiome information, the associated condition, and the secondmicrobiome information, the evaluation including QIIME processing, theQIIME processing including constructing a phylogentic tree, constructinga BIOM table, UniFac, and PCoA; whereby the evaluation identifies aproduction characteristic of the well; and, controlling the productionof hydrocarbons from the well based at least in part upon the identifiedproduction characteristic.

Moreover there is provided the present systems, operations and methodshaving one or more of the following features: wherein the identifiedproduction characteristic is selected from the group consisting of watercut, zone production, change in zone production, and non-biologic changein production.

Additionally there is provided a method of forming a borehole in theearth for the recovery of hydrocarbons, the method including: locating arig at a well site; circulating a fluid in a borehole at the well site,whereby material from within the borehole is removed from the boreholeby the fluid; obtaining a sample of the fluid; analyzing the sample;obtaining microbiome information of the sample; and, performing anevaluation on the microbiome information, whereby the evaluationprovides directing information to direct the formation of the borehole.

Still further there is provided the present systems, operations andmethods having one or more of the following features: wherein theanalysis includes extracting material including genetic materialselected from the group consisting of a SSU rRNA gene 16S, SSU rRNA gene18S, LSU rRNA gene 23S, LSU rRNA 28S, ITS in the rRNA operon, and ITS inthe rRNA cpn60; wherein, the microbiome information is selected from thegroup consisting of historic microbiome information, real timemicrobiome information, derived microbiome information, predictivemicrobiome information; wherein the analysis includes selection andsequencing of the material; wherein the information relates to a payzone; wherein the information relates to a pay zone; wherein theanalysis includes preparation of libraries; wherein directing theformation of the borehole including a modification to the drilling plan;wherein directing the formation of the borehole including locating theborehole in a particular position within formation; wherein directingthe formation of the borehole including locating the borehole in aparticular position within formation; and, wherein directing theformation of the borehole including an activity selected from the groupconsisting of placing a plug, creating a brank, side tracking,determining the depth of the borehole, a casing plan, determining thelocation of perforations, determining the placement of perforations,following a lateral hydrocarbon containing formation, and secondaryrecovery from the borehole.

Still further there is provided a method of forming a borehole in theearth for the recovery of hydrocarbons, the method including: creating aborehole in the earth at the well site; advancing the borehole andcirculating a drilling fluid, whereby material from within the boreholeis removed from the borehole by the drilling fluid; obtaining a sampleof the drilling fluid; analyzing the sample; obtaining microbiomeinformation of the sample; and, performing an evaluation on themicrobiome information, whereby the evaluation provides directinginformation to direct the formation of the borehole.

Further there is provided the present systems, operations and methodshaving one or more of the following features: wherein the sample foranalysis consists essential of material removed from within theborehole; wherein the solids are essentially separated from the drillingfluid, and the analysis is performed on at least one of the separatedsolids or fluid; wherein the analysis includes providing a phylogenetictree; wherein the analysis includes a correction step; wherein theanalysis includes an extraction procedure selected from the groupconsisting of beating, sonicating, freezing and thawing, and chemicaldisruption; wherein the analysis includes amplification of at least aportion of the material; wherein the microbiome information includesinformation obtained from variable regions of the 16S rRNA; wherein thevariable regions are selected from the group consisting of V2, V4, andV6; and wherein directing the formation of the borehole including anactivity selected from the group consisting of placing a plug, creatinga brank, side tracking, determining the depth of the borehole, a casingplan, determining the location of perforations, determining theplacement of perforations, following a lateral hydrocarbon containingformation, and secondary recovery from the borehole.

Yet additionally there is provided a method of evaluating and planningan oil field to optimize the placement of wells and recovery ofhydrocarbons from the field, the method including: obtaining microbiomeinformation of a plurality of samples from selected locations in ahydrocarbon containing formation beneath the field of the sample; and,performing an evaluation on the microbiome information, whereby theevaluation provides directing information to direct the placement ofwells in the field.

Further there is provided the present systems, operations and methodshaving one or more of the following features: wherein the analysisincludes providing a phylogenetic tree; wherein the analysis includesproviding a genetic barcode to a sample of the material; wherein themicrobiome information includes a OTU; wherein the microbiomeinformation defines a biogeographical pattern; wherein the microbiomeinformation includes information obtained from variable regions of the16S rRNA; wherein the variable regions are selected from the groupconsisting of V2, V4, and V6; wherein the evaluation includes forming ann-dimensional plot, where n is selected from the group of integersconsisting of 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, and 14; wherein theevaluation includes measuring a change in gene sequences and using themeasured change as a molecular clock in the evaluation to determine therelated nature of material; and, wherein the evaluation includesmeasuring a change selected from the group consisting of a change ingene sequences, and change in gene sequences and using the measuredchange as a molecular clock in the evaluation to determine the relatednature of material.

Still further there is provided a method of hydraulically fracturing aformation for the recovery of hydrocarbons, the method including:obtaining microbiome information of a sample of fracturing fluid; and,performing an evaluation on the microbiome information, whereby theevaluation provides directing information to direct a fracturingoperation in the well.

Additionally there is provided a method of forming a borehole in theearth for the recovery of hydrocarbons, the method including: obtainingmicrobiome information from a sample of a circulation fluid from aborehole; and, performing an evaluation on the microbiome information,whereby the evaluation provides directing information to direct therecovery of a material from the borehole.

There is additionally provided a port on a drilling fluid return line,the port having a pressure reducing value, and a nipple for the sterileattachment to a sampling container.

Still further there is provided an oil field microbiometric sequencingfield unit including: sample collection containers; personal protectiveequipment; pipettors; electrophoresis equipment; fluorometric measuringdevices; centrifuges; PCR hoods; thermocylers; cooling and heating unitfor 96 well plates; DNA/RNA extraction reagents; quantification reagentsfor genetic material; liquid-handling robot; sequencer; computeresources; and, high speed data transmission capabilities.

Additionally there is provided the present systems, operations andmethods having one or more of the following features: wherein thedirecting information includes oil saturation and permeability data;wherein the directing information includes well wettability data;wherein the directing information includes data for a well feature, thewell feature selected from the group consisting of oil viscosity,temperature, pressure, porosity, oil saturation, water saturation, andcompressibility; wherein the directing information includes subsurfaceflow communication and reservoir connectivity data; wherein thedirecting information includes propensity for producing oil versus gasdata; wherein the directing information includes data about theproduction zone that improves vertical and aerial conformance; whereinthe directing information includes chemical and physical properties of atreatment fluid; wherein the directing information includes chemical andphysical properties of a production fluid; wherein the directinginformation includes environmental impact data wherein the directinginformation includes data for a high resolution subsurface geologic mapof a production zone; wherein the directing information includesoil-water contact level data; wherein the directing information includesdata on the likelihood of oil coning or cusping; wherein the directinginformation includes lease valuation data; wherein the directinginformation includes recovery factor data; wherein the directinginformation includes predictive data regarding the existence of H₂S in awell; wherein the directing information includes predictive data for afuture potential oil reservoir; wherein the directing informationincludes oil saturation and permeability data; wherein the directinginformation includes well wettability data; wherein the directinginformation includes data for a well feature, the well feature selectedfrom the group consisting of oil viscosity, temperature, pressure,porosity, oil saturation, water saturation, and compressibility; whereinthe directing information includes subsurface flow communication andreservoir connectivity data; wherein the directing information includespropensity for producing oil versus gas data; wherein the directinginformation includes data about the production zone that improvesvertical and aerial conformance; wherein the directing informationincludes chemical and physical properties of a treatment fluid; whereinthe directing information includes chemical and physical properties of aproduction fluid; wherein the directing information includesenvironmental impact data; wherein the directing information includesdata for a high resolution subsurface geologic map of a production zone;wherein the directing information includes oil-water contact level data.

Yet further there is provided the present systems, operations andmethods having one or more of the following features: wherein thedirecting information is selected from the group consisting of oilsaturation data, permeability data, well wettability data, oil viscositydata, temperature data, porosity data, water saturation data,compressibility data, subsurface flow communication data, reservoirconnectivity data, vertical conformance data, aerial conformance data,oil coning data, oil cusping data, lease valuation data, recovery factordata, and H₂S data.

Still further there is provided the present systems, operations andmethods having one or more of the following features: wherein thedirecting information is selected from the group consisting of oilsaturation data, permeability data, well wettability data, oil viscositydata, temperature data, porosity data, water saturation data,compressibility data, subsurface flow communication data, reservoirconnectivity data, vertical conformance data, aerial conformance data,oil coning data, oil cusping data, lease valuation data, recovery factordata, and H₂S data.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a perspective view of an embodiment of a drilling site inaccordance with the present inventions.

FIG. 1A is a perspective view of an embodiment of the bell nipplearrangement of the embodiment of FIG. 1.

FIG. 2 is a cross-sectional and perspective view of an embodiment of aborehole and drilling mud handling system in accordance with the presentinventions.

FIG. 3 is a perspective view of an embodiment of an embodiment of ahydraulic fracturing site in accordance with the present inventions.

FIG. 4 is a flow chart of an embodiment of a process in accordance withthe present inventions.

FIG. 5 is a flow chart of an embodiment of a process in accordance withthe present inventions.

FIG. 6 is an illustration of an embodiment of barcoded primers forhigh-throughput sequencing in accordance with the present inventions.

FIG. 7 is an illustration of an embodiment of polymerase chain reaction(PCR) in accordance with the present inventions.

FIG. 8 is a chart of an illustration of an embodiment of a power lawgraph in accordance with the present inventions.

FIG. 9 is a graph and illustration of an embodiment of a matrix inaccordance with the present inventions.

FIG. 10 is chart of an embodiment of the association of environmentalparameters with microbial composition in accordance with the presentinventions.

FIG. 11 is a chart of an embodiment of the association of environmentalparameters with microbial composition in accordance with the presentinventions.

FIG. 12 is an embodiment of a Principal Coordinates (PCoA) plot inaccordance with the present inventions.

FIG. 13 is an embodiment of a Principal Coordinates (PCoA) plot inaccordance with the present inventions.

FIG. 14 is an illustration of an embodiment of microbiome compositionpresented in accordance with an embodiment of the present inventions.

FIG. 15 is an illustration of a power law distribution in accordancewith an embodiment of the present inventions.

FIG. 16 is a cross sectional perspective view of an embodiment of an oilfield in accordance with the present inventions.

FIG. 17A is a cross sectional view of an embodiment of an oil field witha well in accordance with the present inventions.

FIG. 17B is a representation of an embodiment of a finger print from thewell of FIG. 17A in accordance with the present inventions.

FIG. 17C is an image of a finger print for the well of FIG. 17A inaccordance with the present inventions.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

In general, the present inventions relate to methods, systems andprocesses for the utilization of microbial and DNA-related informationas well as the determination and relative characterization of microbesand genetic material for use in the exploration and production ofnatural resources in industrial settings. These industrial settingsinclude the exploration, determination, and recovery of naturalresources, including minerals, and energy sources, such as hydrocarbonsincluding oil and natural gas. Further, specific fields for theseindustrial settings for the present invention would include, forexample, energy exploration and production including all phases of wellplanning, construction, completion, production, intervention andworkover, and decommissioning including perforation and hydraulicfracturing and reservoir management.

Thus, microbes and genetic material exist in energy, hydrocarbon, and inparticular oil and natural gas exploration and production, settings,sites or environments. Such microbes and genetic material range fromhistoric, e.g., archaeological sources, from the surface to deep withinthe earth, the air, and essentially within any location that has notbeen sterilized (and even in such settings genetic material that may beuseful for analysis may be present). These microbes and their geneticmaterial provide a significant yet largely untapped source ofinformation for monitoring, planning, developing, enhancing improving,and conducting natural resource exploration and production, energyexploration and production, and in particular the exploration andproduction of hydrocarbons.

In general, the present inventions further relate to systems and methodsfor determining and characterizing the microbiomes of natural resourceexploration and production settings, energy exploration and productionsettings, and in particular, settings relating to the exploration andproduction of hydrocarbons; and in particular determining throughrelationship-based processing, which include custom and unique analyticstools and algorithms, data management, cleansing, filtering, and qualitycontrol, which in turn provide information about these energyexploration and production industrial settings. Such characterizedinformation, for example, can have, and be used for, predictive,historical, analytic, development, control and monitoring purposes.

The relationship-based processing utilizing microbiome information mayinclude historic microbiome information, real-time-based microbiomeinformation, derived microbiome information, and predictive microbiomeinformation, and combinations and variations of these. Further, thisrelationship-based processing utilizes these various types of microbiomeinformation in combination with other data and information such as GPSdata; traditional industrial automation data, e.g., LWD, MWD, flow rate,temperature, formation pressure; geologic data; and geological data.

This information, data, processing algorithms support software, such ashuman machine interface (HMI) programs and graphic programs, anddatabases, may be cloud-based, locally-based, hosted on remote systemsother than cloud-based systems, contained in or associated with a fieldunit, and combinations and variations of these.

Thus, real-time, derived, and predicted data may be collected and storedand thus become historic data for an ongoing process, setting, orapplication. In this manner, the collection, use, and computationallinks can create a real-time situation in which machine learning can beapplied to further enhance and refine the industrial activities orprocesses. Further, real-time, derived, predictive, and historic datacan be, and preferably is, associated with other data and information.Thus, the microbiome information can be associated with GPS data;location data, e.g., MD, TVD LWD, MWD; formation information; particularcomponents and subsystems in a drilling, fracturing, intervention orother oil field system a stage of a hydraulic fracturing operation;geological parameters including formation permeability and porosity.

Thus, real-time, derived, historic, and predictive microbiomeinformation may be further combined or processed with these othersources of information and data regarding the industrial setting orprocess, e.g., hydrocarbon exploration and production, to providecombined, derived, and predictive information. In this manner, themicrobiome information is used in combination with other data andinformation to provide for unique and novel ways to conduct industrialoperations, to develop or plan industrial operations, to refine andenhance existing industrial operations and combinations of these andother activities.

Preferably, these various types of information and data are combinedwhere one or more may become metadata for the other. In this manner,information may be linked in a manner that provides for rapid,efficient, and accurate processing to provide useful informationrelating to the industrial setting. Thus for example, in forming a well,the MD location down hole may be linked as metadata to the real-timemicrobiome information during drilling and compared with similarlylinked meta-data obtained during hydraulic fracturing. Thus for afurther example in the hydrocarbon exploration and production setting,GPS data, geologic data, TVD data and MD data may be used as metadataassociated with real-time microbiome data obtained from well cuttingreturns. This metadata linked real-time microbiome data is then analyzedduring the advancement of the borehole to determine the characterizationof the formation and a perforation and hydraulic fracturing plan toimprove production. Thus, for an example in an exploration andproduction hydrocarbon setting, microbiome data obtained from wellcutting returns may be used as metadata and associated with real-timeGPS data, geologic data, and measured total depth data. Thismetadata-linked historic microbiome data is then analyzed during theadvancement of the borehole, potentially in conjunction with real-timedata, to determine the characterization of the formation and aperforation and hydraulic fracturing plan to improve production.

Additionally, microbiome data can be associated with publicallyavailable, proprietary and combinations of both, information aboutformations and natural resource. Thus, for example a large energycompany having considerable information about the value, size andlocation of its oil field reserves, could combine its proprietaryinformation with microbiome information, and greatly enhance, amongother things, the accuracy of the evaluation of its holdings, as wellas, the ability to recover greater amounts of those holdings from theearth. Further, such microbiome information could be combined withpublically available information and provide enhanced ability to valuethe holdings of the energy company, and thus, form a basis forinvestment decisions in the that energy company. This use of microbiomeinformation in economic analysis may be directed to may othersituations, in addition to a single energy company. Thus, thismicrobiome economic analysis could be applied to all lease holders for aparticular oil field, it could be applied to an oil field to assist indetermining a value for the reserves in that field, it could be appliedto entities associated with a particular country, or geographic area andit could be applied to industrial setting in addition to the oil field,and energy exploration and production.

Thus it is understood that microbiome information may be used asmetadata or may be the underlying information with which the metadata isassociated. Further, in creating larger databases it may be advantageousto have the ability to disassociate some metadata from the underlyinginformation. In this manner, historic microbiome information may becollected which has far greater utilization in which companies orindividuals are more willing to participate or contribute yet whichprovides the ability to be utilized in further and improved derived andpredictive activities.

In general, historic microbiome data may be obtained from knowndatabases or it may be obtained from conducting population studies orcensuses of the microbiome for the particular industrial setting. Thussamples of biological materials are collected and characterized. Thischaracterized information is then processed and stored. Preferably, thedata is processed and stored in a manner that provides for ready andefficient access and utilization in subsequent steps, often usingauxiliary data structures such as indexes or hashes.

In general, real-time microbiome data may be obtained from conductingpopulation studies or censuses of the microbiome as it exists at aparticular point in time, or over a timeseries, for the particularindustrial setting. Thus samples of biological materials are collectedand characterized. This characterized information is then processed andstored. Preferably, the data is processed and utilized in subsequentsteps or may be stored as historic data in a manner that provides forready and efficient access and utilization in subsequent steps.

Generally, microbiome information may be contained in any type of datafile that is utilized by current sequencing systems or that is auniversal data format such as for example FASTQ (including qualityscores), FASTA (omitting quality scores), GFF (for feature tables), etc.This data or files may then be combined using various software andcomputational techniques with identifiers or other data, examples ofsuch software and identifiers for the combining of the various types ofthis information include the BIOM file format and the MI(x)S family ofstandards developed by the Genomic Standards Consortium. For example,information from a programmable logic controller (PLC) in an industrialsetting may be combined with microbial information for storage orfurther processing. Similarly, information from measuring-while-drilling(MWD), logging-while-drilling (LWD), and M/LWD which is provided inknown formats and has known user interfaces may be combined withmicrobiome information for display and analysis in subsequentprocessing. Additionally by way of example, in agricultural settings,data from a harvesting combine regarding yield, microbiome information,and commodities price information may be displayed or stored or used forfurther processing. The combination and communication of these varioussystems can be implemented by various data processing techniques,conversions of files, compression techniques, data transfer techniques,and other techniques for the efficient, accurate, combination, signalprocessing and overlay of large data streams and packets.

In general, real-time, historic, and combinations and variations of thismicrobiome information is analyzed to provide a census or populationdistribution of various microbes. Unlike conventional identification ofa particular species that is present, the analysis of the presentinvention determines in an n-dimensional space (a mathematical constructhaving 2, 3, 5, 12, 1000, or more dimensions), the interrelationship ofthe various microbes present in the system, and potentially alsointerrelationship of their genes, transcripts, proteins and/ormetabolites. The present inventions provide further analysis to thisn-dimensional space information, which analysis renders this informationto a format that is more readily usable and processable andunderstandable. Thus, for example, by using the techniques of thepresent invention, the n-dimensional space information is analyzed andstudied for patterns of significance pertinent to a particularindustrial setting and then converted to more readily usable data suchas for example a 2-dimensional color-coded plot for presentation througha HMI (Human-Machine Interface).

Additionally, the n-dimensional space information may be related, e.g.,transformed or correlated with, physical, environmental, or other datasuch as the presence of a mineral or the geologic time period andconditions under which a particular formation was created, either byprojection into the same spatial coordinates or by relation of thecoordinate systems themselves, or by feature extraction or other machinelearning or multivariate statistical techniques. This relatedn-dimensional space information may then be further processed into amore readily usable format such as a 2-dimensional representation.Further, this 2-dimensional representation and processing may, forexample, be based upon particular factors or features that are ofsignificance in a particular industrial setting. The 2-dimensionalinformation may also be further viewed and analyzed for determiningparticular factors or features of significance for a system. Yetfurther, either of these types of 2-dimensional information may be stillfurther processed using for example mathematical transformationfunctions to return them to an n-dimensional space which mathematicalfunctions which may be based upon known or computationally determinedfactors or features.

Thus the present inventions provide for derived and predictedinformation that can be based upon the computational distillation ofcomplex n-dimensional space microbiome information, which may be furthercombined with other data. This computationally distilled data orinformation may then be displayed and used for operational purposes inthe industrial setting, it may be combined with additional data anddisplayed and used for operational purposes in the industrial setting,it may be alone or in combination with additional information subjectedto trend, analysis, to determine features or factors of significance, itmay be used for planning and operational purposes in combinations andvariations of these and other utilizations.

Turning to FIG. 1 there is shown an embodiment of a drilling rig sitefor the drilling of an oil well. Thus, the drilling rig 100 has aderrick 101, having a crown block 102, a traveling block 103, a topdrive, 104, a drawworks 105, a drill line 106, and a rotary table 109.The derrick 101 is positioned upon an elevated rig floor 108. (It beingunderstood that this is a simplified representation of a drilling rig,and that other components, that are known to the art, such as monkeyboard, dog house, elevators, pumps, manifolds, lines, iron roughnecks,kellys, etc., may be present. Further, other types of drilling rigs,such as masts, and rams, etc., may be used.) The drilling rig 100 has apipe handling system 110 for bring drilling pipe and drilling stringsfrom a holding area to the rig floor 108. The drilling rig 100, has adrill string 107 positioned in the top drive 104, and extending throughthe rotatory table 109, the bell nipple 129, below the rig floor 108(and better seen in FIG. 1A), a BOP 123, and down into a borehole (notshown in the figure). Turning the FIG. 1A there is shown the embodimentof the BOP 123 and bell nipple 129 that are located below the rig floor108. The bell nipple 129 is attached by for example a bolted flange to aflange on an annular preventer 124, which is connected, by boltedflanges, to one or more ram shears, e.g., 125. Ram shears would includeany mechanical devices that clamp, grab, hold, cut, sever, crush, orcombinations thereof, a tubular within a BOP stack, such as shear rams,blind rams, variable rams, variable pipe rams, blind-shear rams, piperams, casing shear rams, and preventers such as Hydril's HYDRIL PRESSURECONTROL COMPACT Ram, Hydril Pressure Control Conventional Ram, HYDRILPRESSURE CONTROL QUICK-LOG, and HYDRIL PRESSURE CONTROL SENTRY Workover,SHAFFER ram preventers, and ram preventers made by Cameron.

The BOP 123 has choke 127 and kill 126 lines. These lines are associatedwith a manifold assembly 128, and are used to provide drilling mud,e.g., heavy mud, into the well to address pressure management, includingsituations, such as a well kick, and emergency pressure and flowsituations.

An electrical generator 111, supplies power to the rig by variouselectrical lines, e.g., electric race way 112.

During drilling the top drive 104 rotates the drill string 107 that hasa drill bit (not shown) at its distal end, and which is engaged againstthe bottom of the borehole to advance the borehole. Weight is providedto the drill bit (weight-on-bit (“WOB”) through for example the use ondrilling collars.

During drilling, as well as at other times when the well is beingcirculated, drilling mud is pumped by mud pump assembly 114 to drillingmud line 113 which is connected to flexible inlet mud hose 122, whichprovide the mud to the top drive, where the mud is directed down theinterior of the drill string 107. The mud is pumped down the drillstring 107, to the drill bit and out the drill bit, where is carriesaway the cuttings from the advancement of the borehole. The drillingmud, mixed with the cuttings, returns up the annulus between theborehole wall and the drill string. (Note the mud or any drilling orsampling fluid can also be circulated while the bit is not rotating, andthe circulation can be a reverse circulation as well.) The returningdrilling mud and cuttings can be sampled, for example, from mud returnline 120, at for example sample point 120 a. Sample point 120 a may belocated anywhere along the mud return line 120 that is safe andconvenient to obtain the samples.

Mud return line 120 delivers the mud and cuttings to a shaker or screenassembly 119, which begin the separation and clean of the drilling mud.A sample of the removed solids can be obtained from sample point 119 a.Gas from the mud is separated from by the mud/gas separator 117. Thedrilling mud is then delivered by line 121 to a mud pit, (e.g., holdingpond, tanks, etc.) 118. Samples may be taken from sample point 118 a.

The mud handling system additionally has water storage tanks 115, mudholding tanks 116 (as well as other holding tanks, chemical storage,etc., not shown in the figure).

Drilling mud (which should be given its broadest definition and willinclude all types of drilling fluids) can generally be liquid, gas, andfoam. Different types of drilling mud may be used during the formationof a borehole, depending upon the conditions and requirements fordrilling the well. Drilling mud can include: freshwater systems;saltwater systems (e.g., brine); oil- or synthetic-based systems (e.g.,diesel), and pneumatic systems (e.g.; air, mist, foam, gas) “fluid”systems. Water-based muds are the most widely used systems. Oil-basedsystems and synthetic bases systems are typically invert-emulsion havingan oil or synthetic base fluid as the continuous (or external) phase,and brine as the internal phase.

Water-based drilling muds may generally be fresh water, seawater, brine,saturated brine, or a formate brine. The type of fluid selected dependson anticipated well conditions or on the specific interval of the wellbeing drilled. For example, the surface interval typically is drilledwith a low-density water- or seawater-based mud that contains fewcommercial additives. These systems incorporate natural clays in thecourse of the drilling operation. Some commercial bentonite orattapulgite also may be added to aid in fluid-loss control and toenhance hole-cleaning effectiveness.

Water based system typically can be nondispersed systems and dispersedsystems.

Nondispersed sytems generally are simple gel-and-water systems used fortophole drilling are nondispersed, as are many of the advanced polymersystems that contain little or no bentonite. The natural clays that areincorporated into nondispersed systems are managed through dilution,encapsulation, and/or flocculation. A properly designed solids-controlsystem can be used to remove fine solids from the mud system and helpmaintain drilling efficiency. The low-solids, nondispersed (LSND)polymer systems rely on high- and low-molecular-weight long-chainpolymers to provide viscosity and fluid-loss control. Low-colloidalsolids are encapsulated and flocculated for more efficient removal atthe surface, which in turn decreases dilution requirements. Speciallydeveloped high-temperature polymers are available to help overcomegelation issues that might occur on high-pressure, high-temperature(HP/HT) wells. With proper treatment, some LSND systems can be weightedto 17.0 to 18.0 ppg and run at 350° F. and higher.

Dispersed systems, generally, are water-based systems that are treatedwith chemical dispersants that are designed to deflocculate clayparticles to allow improved rheology control in higher-density muds.Widely used dispersants include lignosulfonates, lignitic additives, andtannins. Dispersed systems typically require additions of caustic soda(NaOH) to maintain a pH level of 10.0 to 11.0. Dispersing a system canincrease its tolerance for solids, making it possible to weight up to20.0 ppg. The commonly used lignosulfonate system relies on relativelyinexpensive additives and is familiar to most operator and rigpersonnel. Additional commonly used dispersed muds include lime andother cationic systems.

Generally, saltwater drilling fluids often are used for shale inhibitionand for drilling salt formations. They also are known to inhibit theformation of ice-like hydrates that can accumulate around subseawellheads and well-control equipment, blocking lines and impedingcritical operations. Solids-free and low-solids systems can beformulated with high-density brines, such as: calcium chloride; calciumbromide; zinc bromide; potassium and cesium formate; and polymerdrilling fluids

Generally, polymer drilling fluids are used to drill reactive formationswhere the requirement for shale inhibition is significant. Shaleinhibitors frequently used are salts, glycols and amines, all of whichare incompatible with the use of bentonite. These systems typicallyderive their viscosity profile from polymers such as xanthan gum andfluid loss control from starch or cellulose derivatives. Potassiumchloride is an inexpensive and highly effective shale inhibitor that iswidely used as the base brine for polymer drilling fluids in many partsof the world. Glycol and amine-based inhibitors can be added to furtherenhance the inhibitive properties of these fluids.

Typically, barite can be used to increase system density, and speciallytreated organophilic bentonite is the primary viscosifier in mostoil-based systems. The emulsified water phase also contributes to fluidviscosity. Organophilic lignite, asphaltic and polymeric materials areadded to help control HP/HT (High pressure/High temperature) fluid loss.Oil-wetting is essential for ensuring that particulate materials remainin suspension. The surfactants used for oil-wetting also can work asthinners. Oil-based systems usually contain lime to maintain an elevatedpH, resist adverse effects of hydrogen sulfide (H₂S) and carbon dioxide(CO₂) gases, and enhance emulsion stability.

Typically, shale inhibition is one of the key benefits of using anoil-based system. The high-salinity water phase helps to prevent shalesfrom hydrating, swelling, and sloughing into the wellbore. Mostconventional oil-based mud (OBM) systems are formulated with calciumchloride brine, which appears to offer the best inhibition propertiesfor most shales.

Generally, the ratio of the oil percentage to the water percentage inthe liquid phase of an oil-based system is called its oil/water ratio.Oil-based systems generally function well with an oil/water ratio in therange from 1/99 to 99/1, but typically may be 65/35 and may generallyhave an observed range from 70/30 to 90/10.

The foregoing description of drilling mud is a general description, andit is recognized that other types and forms of drilling muds are known,and may be developed, formulated or used.

Turning to FIG. 2 there is shown a cross section and perspective view ofa bore hole and drilling mud system. Thus, the top drive 202 has apassage 216 for providing drilling mud into the drill pipe 203 that islocated in the top drive 202 and which drill pipe 203 is the top pipe indrill string 210. Drill string 210 extends from the top drive 202 belowthe rig floor 201 into a diverting apparatus 213, e.g., a bell nipple,into the BOP 212, and then into bore hole 204. Bore hole 204 is locatedin a formation 205 below the surface of the earth 206. The bore hole 204has an upper casing 207, and an intermediate casing 208. The drillstring 210 has a drill bit 211 that is engaged against and drilling thebottom 209 of the bore hole 204.

The flow of the drilling mud is shown by the various arrows in FIG. 2.Thus, the drilling mud flows down the interior of the drill string 210,through and out of the drill bit 211, where it carries away the cuttingsand moves up the borehole 204 in the annulus formed between the boreholewalls and the drill string. The returning drilling mud and cuttingstravel up through the BOP and directed by the diverting assembly 213into of return line 214. Return line 214 delivers the drilling mud andcuttings to the mud system 200.

A sample port 214 a to obtain a sample for microbiometric analysis ofthe returns is provided in line 214. Line 214 delivers the returns,e.g., drilling mud and cuttings, to a shaker, or shaker table or system,219, having sampling ports 215 a and 215 b. The shaker table 215separates solid from the drilling mud. Thus, sample port 215 a wouldhave sample material that of high solids, and sample point 215 b wouldhave liquid drilling fluid that has had a substantial amount of thesolids removed from it. From the shaker the drilling mud is deliver intoa settling pit or tank 216, which also has a sampling ports 216 a, and216 b. Where sample material 216 b is lower in the tank 216 and thuswould provide a sample of heavier materials that have settled out, andsample port 216 a is higher in the tank 216 and thus would providelighter weight materials.

The drilling mud is then delivered to degasser 217, having sampling port217 a. From the degasser 217 the drilling mud is delivered to a primarycyclonic cleaner bank 218 and to a secondary cyclonic cleaner bank 219.Sample ports 218 a, 218 b, 219 a, 219 b, 219 c are associated with thetwo cleaner banks, to obtain samples of the drilling mud and the variousmaterials that are being separated from the drilling. The drilling mudis then delivered to a mud centrifuge 220, which has a sample collectionpoint 220 a. From the centrifuge 220 the mud is delivered to a mud pit221, having a sample port 221 a. Drilling mud from the mud pit 220 flowinto centrifugal pumps 225, 226, which feed mud pumps 228, 229 (whichcan be duplex, or triplex pump assemblies). Various, feed or make uplines 223, 226, 222 are provided to add material, chemicals, fluids,etc., to the drilling mud.

The mud pumps 228, 229 pump the mud through a pulse dampener 230 andfrom there it is delivered to the top drive and drill string. A sampleport 229 a is provided in the high pressure line leaving the mud pumps.

It being understood that the mud handling system 200 is only anillustrative system, and that other pumps, tanks, lines, and otherequipment, and variations thereof, may be used at a drilling site.

These various sample ports can be used to provide samples of differentmaterials for microbiometeric analysis. These ports, and the obtainedsamples may also be used for other types of, e.g., conventional ortraditional, monitoring and analysis, such as pressure, temperature,solids, etc. In this manner both traditional and microbiometricinformation can be obtained in integrated or associated. Further in thismanner as information is obtained about the microbiome for a particularwell, or even a particular MD for the bore hole, different or multiplesample points can be used. These sample points can be associated withother information and the derived and predicative data and informationcan be enhances and expanded. These types of information from multiplewells in a field, or associated with a reservoir, or even a formation orrock type, can then further be associated, to provided addition data andinformation, e.g., historic, real time, derived and predictive.

Turning now to FIG. 3 there is shown a perspective view of a hydraulicfracturing site 301. Thus, positioned near the well head 314 there is amicrobiometric field sampling and analysis unit 302, pumping trucks 306,proppant storage containers 310, 311, a proppant feeder assembly 309, amixing truck 308, and fracturing fluid holding units 312. It isunderstood that FIG. 3 is an illustration and simplification of afracturing site. Such sites may have more, different, and other piecesof equipment such as pumps, holding tanks, mixers, and chemical holdingunits, mixing and addition equipment, lines, valves and transferringequipment, as well as control and monitoring equipment.

The microbiometric field sampling and analysis unit has a sampling line303, that in the figure is shown as attaching to a sampling port on thewell head 314 through an adapter 304. The sampling line 303 may not beused and samples can be collected from various sample points and carriedto the field unit 302. Additionally, multiple sample lines may be used.Further the field unit may be at any hydrocarbon exploration orproduction site, such as the drilling site of the embodiments of FIG. 1or FIG. 2. Additionally, one or more analysis and sampling field unitscould be located at an oil field. Thus, the unit(s) may have samplinglines that allow for continuous monitoring of for example conventionalinformation such as pressure or temperature, while taking samples formicrobiometric analysis. The field units may also have other lead lines,data line, sample lines and the lake for having data transmitted to unitfor compilation, storage, integration and use. Further, the unit canhave satellite or other forms of remote wireless communication,including data, capabilities. The presence of the field unit, while inmany situations could be preferable, is not required, as samples couldbe transported to a field lab, regional lab, or another on site or offsite facility.

The adapter 314 has a high pressure line 305 that transfers highpressure fracturing fluid from the pump trucks 306 into the well. Thefracturing adapter 314 has packers or other pressure managing apparatus.The well head 314 may also have further well control devices associatedwith it, such as a BOP.

Fracturing fluid from holding units 312 is transferred through lines 313to mixing truck 308, where proppant from storage containers 310, 311 isfeed by assembly 309 and mixed with the fracturing fluid. The fracturingfluid and proppant mixture is the transferred to the pump trucks 306, byline 307, where the pump trucks 306 pump the fracturing fluid into thewell by way of line 305.

Samples may be collected from the fracturing fluid as it recovered fromthe well, or returns from the borehole, for microbiometric analysis.

Further, fluids from a well bore, (e.g., hydrocarbons, oil, gas, washes,secondary recovery fluids, etc.) may be sampled and used formicrobiometric analysis in other types of oil filed operations, such asworkover, completion and workover and completion activities, which wouldby way of example include activities that place at or near thecompletion of drilling a well, activities that take place at or the nearthe commencement of production from the well, activities that take placeon the well when the well is producing or operating well, activitiesthat take place to reopen or reenter an abandoned or plugged well orbranch of a well, and would also include for example, perforating,cementing, acidizing, fracturing, pressure testing, the removal of welldebris, removal of plugs, insertion or replacement of production tubing,forming windows in casing to drill or complete lateral or branchwellbores, cutting and milling operations in general, insertion ofscreens, stimulating, cleaning, testing, analyzing and other suchactivities.

Microbiometric sampling and analysis may also take place duringsecondary, tertiary and other types of enhanced recovery activities.Including all types of sweeping, flooding, thermal, microbial,polymeric, chemical and other recovery methods know to those of skill inthe art or later developed.

The sampling for these oil field activities may take place along thelines of the embodiments of FIGS. 1, 2 and 3, with the use of sampleports at various locations up hole to obtain sample from fluids leavingthe borehole, or from holding and separation tanks or stations for suchfluids.

Further, coil tubing, cap strings, tube within a tube, and other typedof small tubulars, (that preferable can be inserted into the borehole,casing, production tubing, etc.; with little to no effect of flowtherein) or other sample lines may be inserted deep within the borehole,or a tubular within the borehole, to a particular and predeterminedlocation to obtain specific samples of materials for microbiometricanalysis from those locations.

In the production of natural resources from formations within the eartha well or borehole is drilled into the earth to the location where thenatural resource is believed to be located. These natural resources maybe a hydrocarbon reservoir, containing water, natural gas, gascondensate, crude oil and combinations of these; it may be a heat sourcefor geothermal energy; or it may be some other natural resource that islocated within the ground.

These resource-containing formations may be a few hundred feet, a fewthousand feet, or tens of thousands of feet below the surface of theearth, including under the floor of a body of water, e.g., below the seafloor. In addition to being at various depths within the earth, theseformations may cover areas of differing sizes, shapes and volumes.

Unfortunately, and generally, when a well is drilled into theseformations the natural resources rarely flow into the well at rates,durations and amounts that are economically viable. This problem occursfor several reasons, some of which are well understood, others of whichare not as well understood, and some of which may not yet be known.

Among other things, it is these previously unknown and poorly understoodreasons for uneconomical flow, sub-par flow and no flow, that themicrobiome information obtained and utilized by the present inventions,including real-time, historic, derived and predictive microbiomeinformation can shed light on, and provide ways to avoid, or improvesuch undesirable flows. Further, the microbiome information can be usedto also better understand economically successful flows of hydrocarbonsfrom well, and through this understanding the present inventions willprovide derived and more preferably predictive microbiome information toreplicate, or otherwise obtain, those flows in other wells and field.Similarly, such microbiome information can be used for well planning andreservoir management purposes.

The ability, or ease, by which the natural resource can flow out off theformation and into the well or production tubing (into and out of, forexample, in the case of engineered geothermal well) can generally beunderstood as the fluid communication between the well and theformation. As this fluid communication is increased several enhancementsor benefits may be obtained: the volume or rate of flow (e.g., gals perminute) can increase; the distance within the formation out from thewell where the natural resources will flow into the well can be increase(e.g., the volume and area of the formation that can be drained by asingle well is increased and it will thus take less total wells torecover the resources from an entire field); the time period when thewell is producing resources can be lengthened; the flow rate can bemaintained at a higher rate for a longer period of time; the oil/waterratio can increase that results in lower separation and energy costs;and combinations of these and other efficiencies and benefits.

Fluid communication between the formation and the well can be greatlyincreased by the use of hydraulic fracturing techniques. The first usesof hydraulic fracturing date back to the late 1940s and early 1950s. Ingeneral hydraulic fracturing treatments involve forcing fluids down thewell and into the formation, where the fluids enter the formation andcrack, e.g., force the layers of rock to break apart or fracture. Thesefractures create channels or flow paths that may have cross sections ofa few micron's, to a few millimeters, to several millimeters in size,and potentially larger. The fractures may also extend out from the wellin all directions for a few feet, several feet and tens of feet orfurther. It should be remembered that the longitudinal axis of the wellin the reservoir may not be vertical: it may be on an angle (eitherslopping up or down) or it may be horizontal. For example, in therecovery of shale gas the wells are typically essentially horizontal inthe reservoir. The section of the well located within the reservoir,i.e., the section of the formation containing the natural resources, canbe called the pay zone. As the fracturing fluids extend out from thewell they will capture, e.g., pick up, dissolve (especially ifacidizing), and carry along biological and genetic material that isfound in the formation and exposed to the fracturing fluid by thebreaking open of the rocks. This liquid solution of brine, fracturingfluid, water, other chemicals, and biological and genetic materialfollowing a hydraulic fracturing operation is known as “Flowback”.

Typical fluid volumes in a propped fracturing treatment of a formationin general can range from a few thousand to a few million gallons.Proppant volumes can approach several thousand cubic feet. In generalthe objective of a proppant fracturing is to have uniform proppantdistribution. In this manner a uniformly conductive fracture along thewellbore height and fracture half-length can be provided.

The fluids used to perform hydraulic fracture can range from verysimple, e.g., water, to very complex. Additionally, these fluids, e.g.,fracing fluids or fracturing fluids, typically carry with themproppants. Proppants are small particles, e.g.; grains of sand, that areflowed into the fractures and hold, e.g.; “prop” or hold open thefractures when the pressure of the fracturing fluid is reduced and thefluid is removed to allow the resource, e.g.; hydrocarbons, to flow intothe well. In this manner the proppants hold open the fractures, keepingthe channels open so that the hydrocarbons can more readily flow intothe well. Additionally, the fractures greatly increase the surface areafrom which the hydrocarbons can flow into the well.

The composition of the fluid, the characteristics of the proppant, theamount of proppant, the pressures and volumes of fluids used, the numberof times, e.g., stages, when the fluid is forced into the formation, andcombinations and variations of these and other factors may bepreselected and predetermined for specific fracturing jobs, based uponthe microbiome information, including real-time, historic, derived andpredictive microbiome information alone or more preferably inconjunction with information about the formation, geology, perforationtype, nature and characteristics of the natural resource, formationpressure, and other non-microbiome data points, things or information.

The fluids used to perform hydraulic fracture can range from verysimple, e.g., water, to very complex. Additionally, these fluids, e.g.,fracing fluids or fracturing fluids, typically carry with themproppants: but not in all cases, e.g.; when fracing carbonate formationswith acids. Proppants are small particles, e.g., grains of sand,aluminum shot, sintered bauxite, ceramic beads, resin coated sand orceramics, that are flowed into the fractures and hold, e.g., “prop” orhold open the fractures when the pressure of the fracturing fluid isreduced and the fluid is removed to allow the resource, e.g.,hydrocarbons, to flow into the well. In this manner the proppants holdopen the fractures, keeping the channels open so that the hydrocarbonscan more readily flow into the well. Additionally, the fractures greatlyincrease the surface area from which the hydrocarbons can flow into thewell. Typically fracturing fluids, used for example in shale gasstimulations, consist primarily of water but also have other materialsin them. The number of other materials, e.g., chemical additives used ina typical fracture treatment varies depending on the conditions of thespecific well being fractured. Generally, for shale gas, a typicalfracture treatment will use very low concentrations of from about 2 toabout 15 additives. Each component serves a specific, engineered purposeto meet anticipated well and formation conditions.

Generally the predominant fluids being used for fracture treatments inthe shale plays are water-based fracturing fluids mixed withfriction-reducing additives, e.g., slick water, or slick water fracs.Overall the concentration of additives in most slick water fracturingfluids is generally about 0.5% to 2% with water making up 98% to 99.5%.The addition of friction reducers allows fracturing fluids and proppantto be pumped to the target zone at a higher rate and reduced pressurethan if water alone were used.

In addition to friction reducers, other such additives may be, forexample, biocides to prevent microorganism growth and to reducebiofouling of the fractures; oxygen scavengers and other stabilizers toprevent corrosion of metal pipes; and acids that are used to removedrilling mud damage within the near-wellbore.

Further these chemicals and additives could be one or more of thefollowing, and may have the following uses or address the followingneeds: diluted Acid (≈15%), e.g., hydrochloric acid or muriatic acid,which may help dissolve minerals and initiate cracks in the rock; abiocide, e.g., glutaraldehyde, which eliminates bacteria in the waterthat produce corrosive byproducts; a breaker, e.g., ammonium persulfate,which allows a delayed break down of the gel polymer chains; a corrosioninhibitor, e.g., N,N-dimethyl formamide, which prevents the corrosion ofpipes and equipment; a crosslinker, e.g., borate salts, which maintainsfluid viscosity as temperature increases; a friction reducer; e.g.,polyacrylamide or mineral oil, which minimizes friction between thefluid and the pipe; guar gum or hydroxyethyl cellulose, which thickensthe water in order to help suspend the proppant; an iron control, e.g.,citric acid, which prevents precipitation of metal oxides; potassiumchloride, which creates a brine carrier fluid; an oxygen scavenger,e.g., ammonium bisulfite, which removes oxygen from the water to reducecorrosion; a pH adjuster or buffering agent, e.g., sodium or potassiumcarbonate, which helps to maintain the effectiveness of other additives,such as, e.g., the crosslinker; scale inhibitor, e.g., ethylene glycol,which prevents scale deposits in pipes and equipment; and a surfactant,e.g., isopropanol, which is used to increase the viscosity of thefracture fluid.

Generally and for example, in ascertaining microbiome information theselection and sequencing of particular regions or portions of genetic orgenetically encoded materials may be used, including for example, theSSU rRNA gene (16S or 18S), the LSU rRNA gene (23S or 28S), the ITS inthe rRNA operon, cpn60, and various other segments consisting of basepairs, peptides or polysaccharides for use in characterizing themicrobial community and the relationships among its constituents.

Turning to FIG. 16, there is shown a schematic view of a perspectivecross section of an oil field 1600. The oil field 1600 has a surface ofthe earth 1606 and a formation 1607 below the surface of the earth 1606.The oil field 1600 has three wells, 1601, 1602, 1603, that are producinghydrocarbons, e.g., oil, natural gas, or both. It being understood thatthe oil field could have less, or more wells, that are producing or notproducing.

The wells 1601, 1602, 1603 extend down and into the formation 1607. Thewells have zones that are producing hydrocarbons, e.g., productionzones. Typically, these zones have been perforated and hydraulicallyfractured as well as having other completion activities performed onthem. Thus, well 1601 has zones 1601 a, 1601 b, 1601 c. Well 1602 haszones 1602 a, 1602 b. Well 1603 has zones 1603 a, 1603 b, 1603 c, and1603 d. It being understood that a well could have more and less zones,and that they zone can be of varying distance along the borehole.

During planning and production from the well the placement of the zones,closing of zones and opening of new zones is a factor in enhancing theproduction and efficiency of the well. These factors can in somesituations greatly affect the economics of a well and oil field. Thepresent microbiome techniques and analysis can provide information anddata, e.g., microbiome finger prints, finger prints, about the well,production, and the performance of specific zones in the well. Thesefinger prints can be used to determine the relative production from aspecific zone, and thus for example if a zone needs to be closed,reworked, or a new zone needs to be opened. Further these finger printscan be used to determine and analyze the decline in production. Thus,for example, if the finger prints shows that all zones are stillproducing evenly, e.g., there ratio of production from the zones had notmaterially changed, yet production for the well is declining, it couldindicate that a particular treatments, reworking or other activities areneed to increase production. The analysis and information from thepresent microbiome techniques and information can be used to determinewhether a decline in production, failure to produce is based upon theformation, or a mechanical, or structure problem with the well,completion activities and both.

The wells 1601, 1602, 1603 have a spacing between them, shown by doublearrows 1604, 1605. The analysis and information from the presentmicrobiome techniques and information can be used to determine theoptimum spacing for a particular oil field.

Thus, in an embodiment of activities to enhance the production ofhydrocarbons from well 1603, microbiome information is obtained from thehydrocarbons being produced, this first microbiome information isobtained, e.g., the sample is obtained, at time t₁ from hydrocarbonsproduced from a well. The present microbiome evaluations are performedon this sample and information, e.g., a finger print, for eachproduction zone 1603 a, 1603 b, 1603 c, of the well 1603 at time t₁. Ata later point in time, a second microbiome information from the well1603 is obtained from a sample of hydrocarbons produced from the well,the second sample is taken at time t₂. Time t₁ and t₂ can be space intime by one day, two days, a week, a month, six months or other timeperiod. The time t₁, t₂, t_(n) can be based on changes in production,thus the sampling is driven by an event. The sampling may also be partof, and preferably, is part of a route sample and microbiome monitoringand analysis for the well. In this manner a substantial history ofinformation and data can be built for the well, and the oil field.

In this manner, the microbiome information that is used can be historicmicrobiome information, real time microbiome information, derivedmicrobiome information, predictive microbiome information andcombinations and variations of these. The historic microbiomeinformation, in embodiments can be from the Earth Microbiome Project,the Human Microbiome Project, American Gut, GreenGenes, the RibosomalDatabase Project, the International Nucleotide Sequence DatabaseCollaboration (INSDC), American Gut, stored real time data from thewell, and combinations and variations of these.

Preferably, in embodiments of this evaluation of field 1600 and thewells 1601, 1602, 1603 the evaluation links or relates microbiomeinformation and data with industrial setting, e.g., factors, informationabout the well, such as for example GPS data, location data, systemcomponent identification, subsystem component identification, pumpstation true vertical depth of a well, pH, measured depth of a well,processing stage, geological parameter, formation permeability,viscosity, porosity, pressure, flow, temperature, and combinations andvariations of these and other information.

Thus, by way of example the evaluations can provide comparison data overtime, e.g., directing information, that will lead to, support, or form abasis in whole or in part for well, and filed activities, such asworkover and completion activities, stimulation activities, wellplacement, well shut down, well shut in, zone shut down, reworking awell, reworking a zone, refracturing a well, well spacing, drilling anew well and combinations and variations of these and exploration andproduction activities.

In other embodiments the data and information obtained for theseanalysis and in particular these analysis over time, e.g., comparisondata, directing information, predictive, derived, historic andcombinations and variations of these and other types of data for orrelating to oil saturation and permeability; wettability; oil viscosity,temperature, pressure, porosity, oil or water saturation, andcompressibility; subsurface flow communication and reservoirconnectivity; propensity for producing oil versus gas; production zonethat improves vertical and aerial conformance; chemical and physicalproperties of the treatment and produced fluids; environmental impact ofthe hydraulic fracturing; being transformed into a high resolutionsubsurface geologic map of a production zone; oil-water contact levelsin a well; likelihood of oil coning or cusping; commercial valuation ofnew leases or the commercial valuation of existing leases; the recoveryfactor of the existing and potential future wells as well as theeffectiveness of any enhanced oil recovery techniques; existence of H₂Sin existing and potential future wells; existence of current or futurepotential leaks the oil pipelines; existence or future potentialreservoirs; oil saturation and permeability; subsurface flowcommunication and reservoir connectivity; and combinations andvariations of these and other factors.

In an embodiment of the present activities the monitoring of andproduction of hydrocarbons from a well can be conducted by obtaining amicrobiome information from hydrocarbons produced from a well having aplurality of production zones; and, performing an evaluation on themicrobiome information. This analysis provides information, e.g., amicrobiome finger print that is produced and specific form a pluralityof production zones. Thus, information about each production zone andrelative information about all of the production zones can be obtained.For example the relative production rates from each zone can bedetermined. Preferably, this multiple zone information can be obtainedfrom a single sample of hydrocarbons from the well, multiple samples maybe used as well.

In an embodiment a method of enhancing the production of hydrocarbonsfrom an oil field microbiome information is obtained from hydrocarbonsproduced from a first well, e.g., 1603, in an oil field, e.g., 1600,having a plurality of wells at time t₁. Microbiome information isobtained from hydrocarbons produced from a second well, e.g., 1602, infield 1600 at about time t₂. The times t₁ and t₂ can be the same ordifferent time or day, and can extend over longer and shorter periods oftime. There can be more samples taken of any number of times and timeperiods. The present evaluations and techniques are performed includingfor example a relationship based processing having a related geneticmaterial component and an industrial setting component, and also forexample including a bioinformatics stage, which produces a microbiomefinger print for the first well 1603 at time t₁, and the second well1602 at time t₂. This process can than be repeated for the wells overtime t_(n) to t_(n+1) and for other wells as well. The information, e.g.finger prints, from these processes are analyzed and then based at leastin part on the analysis an activity in the oil field is performed.

In a preferred embodiment the analysis of the fluid from well 1603includes for example extracting material comprising genetic materialselected from the group consisting of a SSU rRNA gene 16S, SSU rRNA gene18S, LSU rRNA gene 23S, LSU rRNA 28S, ITS in the rRNA operon, and ITS inthe rRNA cpn60. In a preferred embodiment the microbiome information caninclude for example information obtained from variable regions of the16S rRNA. This variable regions may be for example selected from thegroup consisting of V2, V4, and V6.

The information obtained from the present analysis, e.g., directinginformation, can be used to direct activities in the oil field, such asfor example: placing a plug, creating a brank, side tracking,determining the depth of the borehole, a casing plan, determining thelocation of perforations, determining the placement of perforations,following a lateral hydrocarbon containing formation, and secondaryrecovery from the borehole.

In general, an embodiment of a method of the present invention mayinclude one or more of the following steps which may be conducted invarious orders: sample preparation including obtaining the sample at thedesignated location, and manipulating the sample; extraction of thegenetic material and other biomolecules from the microbial communitiesin the sample; preparation of libraries with identifiers such as anappropriate barcode such as DNA libraries, metabolite libraries, andprotein libraries of the material; sequence elucidation of the material(including, for example, DNA, RNA, and protein) of the microbialcommunities in the sample; processing and analysis of the sequencing andpotentially other molecular data; and exploitation of the informationfor industrial uses.

For example, turning to FIG. 4, there is shown an example of a flowchartsetting forth various embodiments of these processes applied acrossvarious industrial settings. Thus, sampling 401 is performed. Thesampling may be for example from an agricultural, petroleum, mineral,food, surfaces, air, water, human source or subject. The samples caninclude for example solid samples such as soil, sediment, rock, metalcounters, and food. The samples can include for example liquid samplessuch as petroleum, surface water, and subsurface water. The samples caninclude for example complex fluid and fluid mixtures such as drillingmud, and fracturing fluid. The sample once obtained has the geneticmaterial isolated or obtained from the sample 402, which for example canbe DNA, RNA, proteins and fragments of these.

A library is prepared 403 from the genetic material. In this stage ofthe process the library can be prepared by use of amplification,shotgun, whole molecule techniques among others. Additionally,amplification to add adapters for sequencing, and barcoding forsequences can be preformed. Shotgun by sonication, enzymatic cleavagemay be performed. Whole molecules can also be sued to sequence all DNAin a sample.

Sequencing 404 is performed. Preferably, the sequencing is with ahigh-throughput system, such as for example 454, Illunina, PacBio, orIonTorrent.

Sequence analysis 405 is prepared. This analysis preferably can beperformed using tools such as QIIME Analysis Pipeline, Machine learning,and UniFrac. Preferably, there is assigned a sequence to the sample viabarcode, for among other things quality control of sequence data.

The analysis 405, is utilized in an industrial application 406. Theapplications can include for example, cosmetics, agriculture, animalhusbandry, pharmaceuticals, space exploration, oil, petroleum,geothermal, alternative energy, and production in factories.

Turning to FIG. 5, there is illustrated an embodiment of the generalprocessing and analysis of the biomolecular material, which is step 405of FIG. 4. Thus as generally shown in FIG. 5, and as explained ingreater detail below, generally, the processing and analysis furtherinvolves matching 501 the sequences to the samples, aligning thesequences to each other, and using the aligned sequences to build aphylogenetic tree 502, further distilling the data to form ann-dimensional plot and then a two or three dimensional plot or othergraphical displays, including displays of the results of machinelearning and multivariate statistical routines, and using the two orthree-dimensional plot or other graphical displays to visualize patternsof the microbial communities in a particular sample over time 503.

Although HMI-type presentation of this information is presentlypreferred, it should be understood that such plots may be communicateddirectly to a computational means such as a large computer or computingcluster for performing further analysis to provide predictiveinformation. Thus the matched sequence samples 501 would be an exampleof real-time or historic microbiome information, the phylogenetic tree502 would be an example of derived microbiome information, and portionsof the graphical displays 203 which have derived microbial informationcombined with other data would be an example of predictive microbiomeinformation. Thus, for example, if the information 503 related toexploration and production of hydrocarbons a uniquely colored section503 a (grey scale used for purposes of patent figures) would indicateareas of higher oil saturation and thus predictive information of wheregreater hydrocarbon production would occur. It should be understood thatthe information section 503, if not otherwise predictive of futureprocesses or activities, would merely be derived data.

Generally, a phylum is a group of organisms at the formal taxonomiclevel of Phylum based on sequence identity, physiology, and other suchcharacteristics. There are approximately fifty bacterial phyla, whichinclude Actinobacteria, Proteobacteria, and Firmicutes. Phylum is theclassification that is a level below Kingdom, in terms ofclassifications of organisms. For example, or E. coli the taxonomystring is Kingdom: Bacteria; Phylum: Proteobacteria; Class: Gammaproteobacteria; Order: Enterobacteriales; Family: Enterobacteriaceae;Genus: Escherichia; and Species: coli.

Generally, phylogeny refers to the evolutionary relationship between aset of organisms. This relationship can be based on morphology,biochemical features, and/or nucleic acid (DNA or RNA) sequence. One canmeasure the changes in gene sequences and use that as a molecular clockto determine how closely or distantly the sequences, and hence theorganisms that contain them, are related.

Generally, different methods of microbiotic classification exist. Twogeneral methods are that of phylotypes whereby sequences are classifiedupon reference taxonomic outlines to classify sequences to taxonomicbins; and that of operational taxonomic unit (“OTU”) based methods wheresequences are classified based on their similarity to each other (forinstance an 97% similarity OTUs are roughly analogous to “species”classification). Phylotypes can also be defined at other taxonomiclevels and these other levels are sometimes critical for identifyingmicrobial community features relevant to a specific analysis. Becauseshort DNA, RNA or protein sequences (“reads”) can be used, thesesequences may not accurately identify many organisms to the level ofspecies, or even strain (the most detailed level of phylogeneticresolution, which is sometimes important because different strains canhave different molecular functions). In cases where a “phylotype”matches a sequence or group of sequences from a known organism in thedatabases, it can used to say that a particular sequence is from anorganism like, for example, E. coli.

Generally, a taxon is a group of organisms at any level of taxonomicclassification. Here, taxon (plural: taxa) is a catchall term used inorder to obviate the usage of the organism names repeatedly and toprovide generality across taxonomic levels.

Microbial community diversity and composition may vary considerablyacross industrial environments and settings, and the present inventionslink and or correlate these changes to biotic or abiotic factors andother factors and conditions in the industrial environment to createderived and predictive information. Thus these patterns of microbialcommunities for example geological patterns of microbial communities orpatterns of microbial communities in an industrial system(microbiosystem metrics) which are determined by the present inventioncan give rise to predictive information for use in the industrialsetting.

Examinations of microbial populations, e.g., a census, may provideinsights into the physiologies, environmental tolerances, and ecologicalstrategies of microbial taxa, particularly those taxa which aredifficult to culture and that often dominate in natural environments.Thus, this type of derived data is utilized in combination with otherdata in order to form predictive information.

Microbes are diverse, ubiquitous, and abundant, yet their populationpatterns and the factors driving these patterns were prior to thepresent inventions not readily understood in industrial settings andthus it is believed never effectively used for the purposes forascertaining predictive information. Microorganisms, just likemacroorganisms (i.e.: plants and animals), exhibit no single sharedpopulation pattern. The specific population patterns shown bymicroorganisms are variable and depend on a number of factors,including, the degree of phylogenetic resolution at which thecommunities are examined (e.g., Escherichia), the taxonomic group inquestion, the specific genes and metabolic capabilities thatcharacterize the taxon, and the taxon's interactions with members ofother taxa. Thus, such population patterns can be determined inindustrial settings and utilized as derived data for the purposes ofascertaining predictive information.

However, for certain environments, common patterns may emerge if thebiogeography (e.g., microbial populations for example as determined froma census), of that particular environment is specifically examined. Inparticular, the structure and diversity of soil bacterial communitieshave been found to be closely related to soil environmentalcharacteristics such as soil pH. A comprehensive assessment of thebiogeographical patterns of, for example, soil bacterial communitiesrequires 1) surveying individual communities at a reasonable level ofphylogenetic detail (depth), and 2) examining a sufficiently largenumber of samples to assess spatial patterns (breadth). The studies ofbiogeographical patterns is not limited to soil, and will be extended toother environments, including but not limited to, any part of a livingorganisms, bodies of water, ice, the atmosphere, energy sources,factories, laboratories, farms, processing plants, hospitals, and otherlocations, systems and areas.

It should be understood that the use of headings in this specificationis for the purpose of clarity, and are not limiting in any way. Thus,the processes and disclosures described under a heading should be readin context with the entirely of this specification, including thevarious examples. The use of headings in this specification should notlimit the scope of protection afford the present inventions.

Generally, samples will be collected in a manner ensuring that microbesfrom the target source are the most numerous in the samples whileminimizing the contamination of the sample by the storage container,sample collection device, the sample collector, other target or othernon-target sources that may introduce microbes into the sample from thetarget source. Further, samples will be collected in a manner to ensurethe target source is accurately represented by single or multiplesamples at an appropriate depth (if applicable) to meet the needs of themicrobiome analysis, or with known reference controls for possiblesources of contamination that can be subtracted by computationalanalysis. Precautions should be taken to minimize sample degradationduring shipping by using commercially available liquids, dry ice orother freezing methods for the duration of transit. If appropriate testsare completed, to show that there is no impact of shipping method ortemperature, samples may also be shipped at ambient temperature.

Preferably, precautions, adjustments and general biological materialsampling techniques and most preferably best practices, can be taken orincluded in the sample collection methodology to provided greaterassurances that the collected samples accurately represent themicrobiome from oil and gas wells. As noted in this specification, thecollection containers must be suitable for molecular biological samplerecovery, environmental sample recovery and combinations and variationsof these. In general, similar care must be taken when sampling wellmaterial. Many microbial communities residing in oil and gas fields maybe of low biomass (e.g., relatively few organisms are present per unitvolume or unit of mass) the introduction of organisms from non-targetsources as well as changes in environment may become issues, and in somesituations are important considerations, in managing the resulting data.For instance, samples collected by untrained individuals may result inthe introduction of microbes from sources including, but not limited to,those residing on human skin, surface soils or deeper sediments,drilling mud and injection water. Mitigating the introduction of thesemicrobes into the target samples can be effectively accomplished by theuse of personal protective equipment including, but not limited to,disposable examination gloves, surgical type face masks and sterilecollection containers when each new type of sample from the well or atthe drill site is collected.

The use of external materials used to drill and produce hydrocarbonsfrom a well is inevitable and these sources should be included in athorough assessment of subsurface microbial communities. Liquids such aswater or combinations of water and other liquids, proppant-loadedslurries, acid solutions can be sampled to identify microbes whichreside in these sources so they are not confused with microbes of thesub surface. Similar care as noted above can also be taken when samplingthese sources prior to their injection into the well. The use ofpersonal protective equipment to limit contact between the samplecollector and the sample in many cases will be the most preferredpractice due to low biomass in many of these sources. The use ofdisposable examination gloves cleaned with alcohol or by other means,for instance, during the collection of a similar sample type or a groupof samples from the same source can aid in mitigate the introduction ofnon-target microbes. New gloves and other personal protective equipmentshould be changed for each new or different sample source.

Managing potential sources of non-target microbes can also beaccomplished by monitoring the microbial content of drilling mud (oil orwater based), injection water, well cuttings, flowback or producedwater, formation fluid (oil and water mixes), and oil produced from thewell, among others. Those sources which are injected into the welleither for exploration or production of hydrocarbons should be sampledby trained personnel wearing appropriate personal protective equipmentand collected into containers as described above prior to introductioninto the bore hole or production well. Preferably, samples from eachpotential source should be collected as close to the well head (asinflow or outflow) as possible to identify the potential contribution ofeach source to the target and/or core microbial community.

For example, samples can be collected in sterile,DNA/DNase/RNA/RNase-free primary containers with leak resistant caps orlids and placed in a second leak resistant vessel to limit any leakageduring transport. Appropriate primary containers can include any plasticcontainer with a tight fitting lid or cap that is suitable for work inmicrobiology or molecular biology considered to be sterile and free ofmicrobial DNA (or have as little as possible) at minimum. (However, itshould be noted that human DNA contamination, depending upon the markersor specific type microbe that is being looked at may not present aproblem.) The primary container can also be comprised of metal, clay,earthenware, fabric, glass, plastic, wood, etc. So long as the containermay be sterilized and tested to ensure that it is ideallyDNA/DNase/RNA/RNase-free (or at least contains levels of nucleic acidmuch lower than the biomass to be studied, and low enough concentrationof nuclease that the nucleic acids collected are not degraded), and canbe closed with a tight-fitting and leak resistant lid, cap or top, thenit can be used as a primary container.

The primary container with the sample can then be placed into asecondary container, if appropriate. Appropriate secondary containerscan include plastic screw top vessels with tight fitting lids or capsand plastic bags such as freezer-grade zip-top type bags. The secondarycontainer can also be comprised of metal, clay, earthenware, fabric,glass, plastic, wood, etc. So long as the container can be closed orsealed with a tight-fitting and leak resistant lid, cap or top, then itcan be used as a secondary container. The secondary container can alsoform a seal on itself or it can be fastened shut for leak resistance.

The samples should generally be collected with minimal contact betweenthe target sample and the sample collector to minimize contamination.The sample collector, if human, should generally collect the targetsample using gloves or other barrier methods to reduce contamination ofthe samples with microbes from the skin as discussed above. The samplecan also be collected with instruments that have been cleaned and/orsterilized. The sample collector, if machine, should be cleaned andsterilized with UV light and/or by chemical means prior to each samplecollection. If the machine sample collector requires any maintenancefrom a human or another machine, the machine sample collector must beadditionally subjected to cleaning prior to collecting any samples.

Thus, for example, the outflow of mud return line (120/121) before themud is deposited into the mud pit (118 a—preferably at asterisk labeled214 a in FIG. 2) is collected, because preferably the sample should beas fresh as can be sample from the well. Likewise, the sample may alsobe collected, but then kept on ice, or frozen (and/or kept ambient—ifdeemed acceptable to processes) between sampling and shipping. Thesample is drawn off through valve placed at 214 a into sterile containerby trained personnel wearing sterile exam gloves. The container isfilled to a predetermined volume with well outflow material and apreservative may or may not be added, the sample may be frozenimmediately, shipped and combinations and variations of these. Forexample the sample container can be filled to a predetermined volumewith well outflow material, a preservative added and the sample iscooled and shipped later. Automatic sampling can be accomplished bydiverter valve placed at 214 a into rack that moves sample collectiontubes (with or without preservative added) to collect samples acrossgiven time span or to collect any samples.

Monitoring microbial communities from the sub surface during a hydraulicfracturing operation can consist of samples taken from the high pressureinflow line (FIG. 3, element 315), preferably as close to the fracadapter (element 304) as possible and from the umbilical (element 303)into containers described above. The microbial content of hydraulicfracturing fluid constituents (e.g., water, sand, inorganic and organicchemicals, acids, bases, etc.) can also be monitored prior to theirmixing and injection into the borehole. Pressure reducers/valves mayneed to be installed to collect samples for analysis on element 315.Outflow from the bore hole can be transmitted to a mobile analysis unitvia element 303 for immediate analysis or preserved and shipped to labfor analysis.

Tracers for insertion into the well and then monitoring upon recoveryfrom the well may also be employed. Further, specific samples may betaken, by way of an ESP or other pump type, or tube placed at a specificlocation in a well to monitor activity there.

Two broad classes of control samples, among others, preferably should becollected to monitor the introduction of microbes into the target priorto the initiation of drilling or mixing of chemicals. The first class ofsamples are to monitor the solids and liquids injected, detailed above,into the borehole or well including individual components of hydraulicfracturing fluid, water, sand, inorganic and organic chemicals or anyother solid or liquid material that is injected or is collected from anexploratory or production well. The second class of control samplesshould be derived from local environment which can include but not belimited to surface or subsurface soils, surface or subsurface water,well tailings, hoses, holding tanks, mixing tanks, pumps, and wellcasings. Control samples of liquids or free-flowing solids (e.g. sand,bentonite, surface soil or well tailings) can be collected inappropriate containers (e.g., as described above) and preserved ifnecessary. Control samples from surfaces such as pumps, well casings,and hoses may be collected on sterile swabs suitable for bacterialspecimen collection and preserved if necessary.

For manual sampling, the sampling kit could include but not be limitedto; collection containers, secondary containers, personal protectiveequipment, preservative, indelible marking pens or pre-printed labelsand a shipping container. The number of collection containers and othercomponents should preferably fit neatly into the shipping container andif necessary multiple sampling kits should be used when many samples areto be collected. Collection on sterile swabs can be done directly fromsurfaces or the swab submerged in samples collected in appropriatesterile sampling containers described above.

Automated sampling can be done at specified, regular intervals using anautomated sampling device attached to a diverter line that attaches to ahose, tube, pipe, or tank carrying the material to be sampled. Thediverter line preferably should be changed periodically to minimize thebuildup of microbial biofilms, which may add an additional source ofcontamination onto the target sample and/or source of data regardingcurrent or historical conditions of the fluid flowing through thediverter. Samples should be collected in sterile containers that may ormay not contain a known volume of preservative. Once collected, thesamples should be removed from the automated sampler and stored orshipped for analysis.

After the sample is collected and placed in a primary and secondarycontainer, the samples will be preserved. One method of preservation isby freezing on dry ice or liquid nitrogen to between 4° C. to −80° C.Another method of preservation is the addition of preservatives such asRNAstable®, LifeGuard™ or another commercial preservative, and followingthe respective instructions. So long as the preservation method willallow for the microbial nucleic acid to remain stable upon storage andupon later usage, then the method can be used.

The samples preferably should be shipped in an expedient method to thetesting facility. In another embodiment, the testing of the sample canbe done on location. The sample testing should be performed within atime period before there is substantial degradation of the microbialmaterial within the sample or such that the microbial fraction changesdue to the alteration in the local environment (due to, for instance,the sample container). So long as the sample remains preserved and thereis no substantial degradation of the microbial material, any method oftransport in a reasonable period of time is sufficient.

Tracers, may also be added to the inflow of a sampling catchment toidentify the organisms present in the system that are not from thetarget source. The tracer can be microorganisms or anything that willallow for analysis of the flow path. For example, in an oil setting, atracer can be used to calibrate the effectiveness of a floodingoperation (water, CO₂, chemical, steam, etc.). The tracer can be used todetermine factors such as the amount of injection fluid flowing througheach zone at the production wellbore and the path of the injection fluidflow from the injection site to the production bore. Fixed and stainedbacteria could be added to any fluid that is injected into the well.Fixed cells are dead and thus will not impact the metabolic activity ofthe target microbial communities. Under circumstances in which there arechanges in the microbial tracers, using high throughput sequencingmethods and analysis, like that included in this specification, theability to account for these changes exists. Bacterial stains includebut are not limited to DAPI (4′,6-diamidino-2-phenylindole), SYBR Green,PicoGreen and bacteria stained with these dyes would indicate whichinjection fluid is found along the fractures or the reservoir. Further,tracers such as potassium bromide may be added to any fluid to track theflow of through the fractures or reservoir.

DNA/RNA Extraction

The extraction of genetic material will be performed using methods withthe ability to separate nucleic acids from other, unwanted cellular andsample matter in a way to make the genetic material suitable foramplification, library construction and combinations and variations ofthese. For example, this can be done with methods including one or moreof the following, but not limited to, mechanical disruption such as beadbeating, sonicating, freezing and thawing cycles; chemical disruption bydetergents, acids, bases, and enzymes; other organic or inorganicchemicals. Isolation of the genetic material can be done through methodsincluding one or more of the following, but not limited to, binding andelution from silica matrices, washing and precipitation by organic orinorganic chemicals, electroelution or electrophoresis or other methodscapable of isolating genetic material. Furthermore, due to the specificphysical or chemical properties of a sample, for example heavy clay orhumus, extra methods such as ‘pre-treatments’ could be used to aid inthe isolation of genetic material.

Extractions will be done in an environment suitable to exclude microbesresiding in the air or on other surfaces in the work area where theextraction is taking place. Care will be taken to ensure that all worksurfaces and instruments are cleaned to remove unwanted microbes,nucleases and genetic material. Cleaning work surfaces and instrumentscan include, but is not limited to, spraying and/or wiping surfaces witha chlorine bleach solution, commercially available liquids such as DNAseAWAY™ or RNase AWAY™ or similar substances that are acceptable inroutine decontamination of molecular biology work areas. Furthermore,aerosol barrier pipette tips used in manual, semi-automated or automatedextraction process will be used to limit transfer of genetic materialbetween instruments and samples.

Controls for Reagents for extractions and/or primary containers (whenappropriate) will be tested to ensure they are free of genetic material.Testing of the reagents includes, but is not limited to performingextraction “blanks” where only the reagents are used in the extractionprocedure. When necessary primary collection containers may also betested for the presence of genetic material serving as one type of‘negative control’ in PCR of the genetic material of the sample. Ineither case, testing the blank or negative control may be accomplished,but not limited to, spectrophotometric, fluorometric, electrophoretic,PCR or other assays capable of detecting genetic material. followed bytesting the blank for the presence of genetic material by, but notlimited to, spectrophotometric, fluorometric, electrophoretic, PCR orother assays capable of detecting genetic material.

The mobile extraction lab should preferably contain DNAse/RNase AWAY,paper towels, pipettors, aerosol barrier pipet tips, centrifuge, PCRenclosure, reagents, personal protective equipment, vacuum pump,consumables (tubes, plates, etc), ice machine, water bath or heated dryblock, and waste disposal vessels enclosed in a container in whichfiltered air creates positive pressure. Further pre-assembled extraction‘packs’ containing clean pipettors, aerosol barrier pipet tips,reagents, personal protective equipment, consumables (tubes, plates,etc) and waste disposal vessels can be shipped to sites where a mobilelab is located. A full-service mobile lab, preferably, should containthe above items in addition to, for example, PCR primers, PCR mastermix, thermocyclers, liquid-handling robot, 96 well fluorometer, highsensitivity DNA assay apparatus such as qBit, a Agilent BioAnalyzer,electrophoresis equipment, DNA sequencer and necessary compute resourcesor high-speed network link to such compute resources. The lab preferablyshould also contain all reagents and kits necessary to perform geneticextractions and any necessary laboratory tests. Generally, theextraction can be one of the more critical aspects of sample prep thatwill require skilled labor and potential training.

The methods, techniques and systems described herein can be useful in aplethora of oil field settings. The scope of the information obtainedcan vary, based on the type of goal to be obtained. For example, anembodiment of the methods can be applied on a macro scale, such as,sampling and analysis from all wells through out the world. Embodimentsof the methods can also be applied on a regional scale, for example,sampling and analysis of wells in a region of the United States, or fora particular formation or field. Further, embodiments of the method canbe applied on a local scale, for example, sampling and analysis of alease area. Further, the method can be applied on a well-based scale,for example, sampling and analysis of a producing well, or particularproducing wells in a field. The following examples are provided toillustrate various devices, tools, configurations and activities. Theseexamples are for illustrative purposes, and should not be viewed aslimiting, and do not otherwise limit, the scope of the presentinventions.

Example 1 Collection and Extraction of DNA

Specific examination of microbial biogeography requires collection ofsamples, using the above general guidelines for sample containers, at apredetermined depth using a device to obtain a roughly equivalent amountof sample from each sampling location at the target location(s). Thenumber of samples to be collected will be determined by the spatial andtemporal scales over which microbial communities vary, the effect sizeof different factors that affect the community, and the range ofconditions that need to be tested to ensure that the relevant diversityof the microbial communities is adequately represented in the samples.Further, samples can be analyzed individually or combined to produce acomposite sample to represent the target sites. Samples should bepreserved by storing on ice and shaded from sunlight while in transitfrom the field. Samples can remain at approximately 4° C. for 1-3 daysfor shipping or can be frozen at −20° C. or −80° C. and shipped on dryice. If and only if, it is deemed appropriate samples can also beshipped at ambient temperature. Samples frozen at −80° C. can be storedindefinitely. DNA can be extracted by any method suitable for isolatingthe genetic material from the soil, oil, water, mixtures, andcombinations and variations of these.

Example 2 Crude Oil Sample from Production Well

Triplicate samples from three wells each from three different possibleformations at three time points (t0, t0 plus one week, and t0 plus onemonth) will be collected. The wells will be matched (as much as ispossible) for geological features including production zone and distancebetween the surface and the oil/water interface, and physical andchemical features of the fluid (e.g., temperature, viscosity, pressure,and hydrocarbon composition). One sample from the correspondingcollection tanks will be gathered when each of these samples arecollected. These will be known as the “baseline” samples.

Triplicate samples will also be collected from the wellhead of six wells(n=18), three each from two different single-production-zone wells.These wells will preferably may be matched with the wells sampled forthe baseline samples, but thought to be from different production zones.Triplicate samples will be collected from the wellheads of five wells,each producing from different, known combinations of production zones(n=15).

Personal protective equipment will be donned to reduce contamination asdescribed above. Oil samples will be collected in appropriate sterile 50ml conical tubes containing (which could contain a preservative ifdeemed necessary, such as 10 ml RNAlater DNAlater or other similar typeof material) and then placed in secondary containment to prevent leakageduring transit and preserve the microbes in the sample.

Once the sample(s) are received at an analysis facility or a mobileanalysis station. DNA extractions are performed. For example for singleextractions: (Step 1) 135-150 μl (this amount should be calibrated andoptimized based on the numbers of microorganisms contained in thesamples and the kit or protocol used) sample will be placed in a Beadtube of the DNA extraction kit. (Step 2) 60 μL of Solution C1 will thenbe added to the sample in the Bead Tube and heated to 65° C. for 10minutes. (Step 3) The sample will then be shaken on a vortexer atmaximum speed for 2 minutes using the vortex adapter. After shaking thesample will be centrifuged for 1 minute at 10,000×g and the supernatanttransferred to a clean tube provided with the extraction kit. (Step 4)To the supernatant, 250 μl of Solution C2 will be added and mixed byinverting 5 times and placed on ice for 5 minutes. The sample will thenbe centrifuged for 1 minute at 10,000×g and the supernatant transferredto a new tube provided by with the extraction kit. (Step 5) To thesupernatant, 200 of Solution C3 will be added and mixed by inverting 5times and placed on ice for 5 minutes. The sample will then becentrifuged for 1 minute at 10,000×g and 700 μl the supernatanttransferred to a new tube provided by with the extraction kit. (Step 6)To the supernatant, 1200 μl of Solution C4 will be added and inverted 5times to mix. (Step 7) 625 μl of the sample+C4 solution will be loadedon to a Spin Filter provided with the extraction kit and centrifuged for1 minute at 10,000×g. The Spin Filter will be removed from the catchtube and the eluate discarded followed by replacement of the Spin Filterinto the catch tube. Step 7 will be repeated until the entire volume ofsample+C4 has been passed through the Spin Filter. After the finalvolume of eluate has been discarded, (Step 8) the Spin Filter will beplaced back into the catch tube to which 500 μl Solution C5 will beadded to the spin Filter and centrifuged for 30 seconds at 10,000×g. Theeluate in the catch tube will be discarded and the Spin Filter placedinto the catch tube and centrifuged for an additional 1 minute 10,000×g.(Step 9) The Spin Filter will be placed in a new catch tube to which 100μl Solution C6 will be added to Spin Filter and allowed to incubate atroom temperature for 1 minute. The Spin filter will then be centrifugedfor 30 seconds at 10,000×g and the eluted DNA stored at −20° C. or −80°C. until needed.

In an embodiment for DNA extractions from a large number of samples, amultiple high throughput DNA extraction kit or protocol can be followed.An example of such a protocol can have the following steps: (Step 1)135-150 μL of oil (this amount should be calibrated and optimized basedon the numbers of microorganisms contained in the samples and the kit orprotocol used) from each sample will be placed in each well of a Beadplate of the DNA extraction kit and 750 μL of Bead Solution is thenadded to each well. (Step 2) 60 μL of Solution C1 will then be added toeach sample, the plate is then sealed using a Square Well Mat or othermeans, and then heated to 65° C. for 10 minutes. (Step 3) The Bead plateis placed between aluminum plate adaptors and shaken on a 96 well plateshaker at speed 20 for 2 minutes. After shaking the Bead plate will becentrifuged for 6 minutes at 4500×g. (Step 4) A 96 well plate (call thisPlate #1) is prepared by adding 250 μl aliquots of Solution C2 into eachwell. Plate #1 is then covered with Sealing Tape. The Square Well Mat onthe Bead plate is removed after centrifugation. (Step 5) After removalof the Sealing Tape from Plate #1, the supernatant from the Bead plate(˜400-500 μL) is transferred to Plate #1, and pipetted several times tomix with the solution already in Plate #1. (Step 6) The Sealing Tape isreapplied to Plate #1, which is then incubated at 4° C. for 10 minutesand then centrifuged at room temperature for 6 minutes at 4500×g. Whilecentrifuging, 200 μl Solution C3 is aliquoted into each well of a new 96well plate (call it Plate #3), then covered with Sealing Tape. (Step 7)Sealing Tape is removed from Plate #1 and the supernatant is removed(˜600 μl; avoiding the pellet) and placed into the wells of another new96 well plate (call it Plate #2). (Step 8) Plate #2 is sealed withSealing Tape and the plate is centrifuged at room temperature for 6minutes at 4500×g. (Step 9) After removing the sealing tape from Plates#2 and #3, the entire volume of supernatant (˜600 μl) is transferredfrom Plate #2 to Plate #3; this volume is pipetted up and down 4 times.(Step 10) After the application of Sealing Tape to Plate #3, it isincubated at 4° C. for 10 minutes, and then centrifuged at roomtemperature for 6 minutes at 4500×g. (Step 11) The supernatant (˜750 μl,avoiding the pellet) from Plate #3 is transferred to a new plate (callit Plate #4). (Step 12) After the application of Sealing Tape to Plate#4, it is centrifuged at room temperature for 6 minutes at 4500×g. Whilecentrifuging, aliquot 650 μl of Solution C4 to the wells of a new 2 mLcollection plate (call it Plate #5). (Step 13) The supernatant (up to650 μl max) is then transferred to Plate #5. (Step 14) Add 650 μlSolution C4 again to Plate #5, which is pipetted to mix thoroughly.(Step 15) The Spin Plate filter is then placed on a new 2 mL collectionplate (call it Plate #6) and 650 μl from Plate #5 is placed into eachwell of the Spin Plate. Centrifuge Tape is applied to the Spin Plate.(Step 16) The Spin Plate is centrifuged at room temperature for 5minutes at 4500×g. The flow through is discarded. The Spin Plate isplaced back on Plate #6. (Step 17) Steps 15-16 are repeated until allthe supernatant has been processed through the Spin Plate filter andthen Spin Plate is placed back on Plate #6. (Step 18) 500 μl of SolutionC5-D is added to each well of the Spin Plate and Centrifuge Tape isapplied to the Spin Plate. (Step 19) The plates are then centrifuged atroom temperature for 5 minutes at 4500×g. The flow through is discardedand the Spin Plate placed back on Plate #6. (Step 20) The plates arecentrifuged for 6 minutes at 4500×g. Flow through is again discarded.(Step 21) The Spin Plate is placed on the Microplate included in the kitand 100 μl of Solution C6 is added to each well of the Spin Plate.Centrifuge Tape is applied and the plates are set to rest for 10 minutesat room temperature. (Step 22) The plates are centrifuged at roomtemperature for 7 minutes at 4500×g. The Centrifuge Tape is then removedand thrown away. The wells of the Microplate are then covered with theElution Sealing Mat from the kit. DNA is ready for any future work.

Example 3 Subsurface Sediment from Exploration Borehole

At the target site, samples will be collected from the material broughtto the surface by the drill with the depth of the sample estimated fromthe length of drill inserted into the borehole. Personal protective gearshould be donned to reduce contamination factors discussed above.Approximately 50-100 g of sediment from the drill will be collectedusing an ethanol sterilized metal spatula and placed into a sterilewhirl type bag or large grab of soil will be made using a sterile whirlpack bag that is inside out (for instance the bag is used as it anotherglove) and stored in cooler with ice (or not depending on theenvironmental temperature). The metal spatulas will be wiped clean andethanol sterilized in between the collection of each sample. The sampletemperature should not be kept any warmer than the environment thesamples were collected from, ideally between 4° C. and −80° C. forstorage and shipment, and or ambient temperatures if deemed allowable.

Once the sample(s) are received at an analysis facility or mobiletesting station, DNA will be extracted using, for example, a commercialextraction kit with some modifications, for example, the MoBio™PowerSoil® DNA extraction. For example for single extractions: (Step 1)approximately 0.1 g (this amount should be calibrated and optimizedbased on the numbers of microorganisms contained in the samples and thekit or protocol used) of soil from each sample will be placed in a Beadtube. (Step 2) 60 μL of Solution will then be added to the sample in theBead Tube and heated to 65° C. for 10 minutes. (Step 3) The sample willthen be shaken on a vortexer at maximum speed for 2 minutes using theMoBio™ vortex adapter. After shaking the sample will be centrifuged for1 minute at 10,000×g and the supernatant transferred to a clean tubeprovided with the extraction kit. (Step 4) To the supernatant, 250 μl ofSolution C2 will be added and mixed by inverting 5 times and placed onice for 5 minutes. The sample will then be centrifuged for 1 minute at10,000×g and the supernatant transferred to a new tube provided by withthe extraction kit. (Step 5) To the supernatant, 200 μl of Solution C3will be added and mixed by inverting 5 times and placed on ice for 5minutes. The sample will then be centrifuged for 1 minute at 10,000×gand 700 μl the supernatant transferred to a new tube provided by withthe extraction kit. (Step 6) To the supernatant, 1200 μl of Solution C4will be added and inverted 5 times to mix. (Step 7) 625 μl of thesample+C4 solution will be loaded on to a Spin Filter provided with theextraction kit and centrifuged for 1 minute at 10,000×g. The Spin Filterwill be removed from the catch tube and the eluate discarded followed byreplacement of the Spin Filter into the catch tube. Step 7 Will berepeated until the entire volume of sample+C4 has been passed throughthe Spin Filter. After the final volume of eluate has been discarded,(Step 8) the Spin Filter will be placed back into the catch tube towhich 500 μl Solution C5 will be added to the Spin Filter andcentrifuged for 30 seconds at 10,000×g. The eluate in the catch tubewill be discarded and the Spin Filter placed into the catch tube andcentrifuged for an additional 1 minute 10,000×g. (Step 9) The SpinFilter will be placed in a new catch tube to which 100 μl Solution C6will be added to Spin Filter and allowed to incubate at room temperaturefor 1 minute. The Spin filter will then be centrifuged for 30 seconds at10,000×g and the eluted DNA stored at −20° C. until needed.

In an embodiment DNA extractions from a large number of samples, acommercial protocol or kit with some minor modifications could befollowed, for example the high throughput MoBio™ PowerSoil® protocol.Pretreatments to used prior to extraction protocol, to remove excesssalts, chemicals, and/or metals may be necessary. An example of a sampleprotocol could include (Step 1) approximately 0.1 g (this amount shouldbe calibrated and optimized based on the numbers of microorganismscontained in the samples and the kit or protocol used) ofsoil/water/sediment from each sample will be placed in each well of aBead plate of the DNA extraction kit and 750 μL of Bead Solution is thenadded to each well. (Step 2) 60 μL of Solution C1 will then be added toeach sample the plate is then sealed using a Square Well Mat or othermeans, and then heated to 65° C. for 10 minutes. (Step 3) The Bead plateis placed between aluminum plate adaptors and shaken on a 96 well plateshaker at speed 20 for 2 minutes. After shaking the Bead plate will becentrifuged for 6 minutes at 4500×g. (Step 4) A 96 well plate (call thisPlate #1) is prepared by adding 250 μl aliquots of Solution C2 into eachwell. Plate #1 is then covered with Sealing Tape. The Square Well Mat onthe Bead plate is removed after centrifugation. (Step 5) After removalof the Sealing Tape from Plate #1, the supernatant from the Bead plate(˜400-500 μL) is transferred to Plate #1, and pipetted several times tomix with the solution already in Plate #1. (Step 6) The Sealing Tape isreapplied to Plate #1, which is then incubated at 4° C. for 10 minutesand then centrifuged at room temperature for 6 minutes at 4500×g. Whilecentrifuging, 200 μl Solution C3 is aliquoted into each well of a new 96well plate (call it Plate #3), then covered with Sealing Tape. (Step 7)Sealing Tape is removed from Plate #1 and the supernatant is removed(˜600 μl; avoiding the pellet) and placed into the wells of another new96 well plate (call it Plate #2). (Step 8) Plate #2 is sealed withSealing Tape and the plate is centrifuged at room temperature for 6minutes at 4500×g. (Step 9) After removing the Sealing Tape from Plates#2 and #3, the entire volume of supernatant (˜600 μl) is transferredfrom Plate #2 to Plate #3; this volume is pipetted up and down 4 times.(Step 10) After the application of Sealing Tape to Plate #3, it isincubated at 4° C. for 10 minutes, and then centrifuged at roomtemperature for 6 minutes at 4500×g. (Step 11) The supernatant (˜750 μl,avoiding the pellet) from Plate #3 is transferred to a new plate (callit Plate #4). (Step 12) After the application of Sealing Tape to Plate#4, it is centrifuged at room temperature for 6 minutes at 4500×g. Whilecentrifuging, aliquot 650 μl of Solution C4 to the wells of a new 2 mLcollection plate (call it Plate #5). (Step 13) The supernatant (up to650 μl max) is then transferred to Plate #5. (Step 14) Add 650 μlSolution C4 again to Plate #5, which is pipetted to mix thoroughly.(Step 15) The Spin Plate filter is then placed on a new 2 mL collectionplate (call it Plate #6) and 650 μl from Plate #5 is placed into eachwell of the Spin Plate. Centrifuge Tape is applied to the Spin Plate.(Step 16) The Spin Plate is centrifuged at room temperature for 5minutes at 4500×g. The flow through is discarded. The Spin Plate isplaced back on Plate #6. (Step 17) Steps 15-16 are repeated until allthe supernatant has been processed through the Spin Plate filter andthen Spin Plate is placed back on Plate #6. (Step 18) 500 of SolutionC5-D is added to each well of the Spin Plate and Centrifuge Tape isapplied to the Spin Plate. (Step 19) The plates are then centrifuged atroom temperature for 5 minutes at 4500×g. The flow through is discardedand the Spin Plate placed back on Plate #6. (Step 20) The plates arecentrifuged for 6 minutes at 4500×g. Flow through is again discarded.(Step 21) The Spin Plate is placed on the Microplate included in the kitand 100 μl of Solution C6 is added to each well of the Spin Plate.Centrifuge Tape is applied and the plates are set to rest for 10 minutesat room temperature. (Step 22) The plates are centrifuged at roomtemperature for 7 minutes at 4500×g. The Centrifuge Tape is then removedand thrown away. The wells of the Microplate are then covered with theElution Sealing Mat from the kit. DNA is ready for any future work.

Example 4 Drilling and Hydraulic Fracturing Fluid Collection

Drilling fluid, fracing fluid, oil-water mixtures or any liquid-solidslurry may be collected in large volume sterile containers that followthe teachings of this specifications. Steps will be taken to ensure thata minimum of oil will be involved in the filtration of any watercomponents, as well as additional analyses to subtract out the oilportion of the results, may be warranted. The phases should be allowedto separate and the clear portion can be filtered through 0.22 ummembrane filters to capture the microbes present in the sample. Sampleswith high loads of sand, bentonite, etc can be centrifuged at low speed(less than 1000 rcf) and the supernatant filtered through 0.22 umfilters to capture microbes present in the sample. Filters can be storedfrom 4 to −80 C.

Example 5 Filter Sample Handing

The filters containing microbes should be carefully cut into smallstrips using ethanol-sterilized scissors and forceps on a sterile worksurface such an petri dish located in a suitable clean work environment.Once cut, a portion of the strips can be loaded into the MoBio bead tubeor into a well on a 96 well bead plate. DNA extraction can proceed asnoted in above for either single or high-throughput extraction methods.The remaining filter strips can be stored at −20 to −80° C. for futureuse if desired.

Library Preparation

Amplification

Genetic material from the samples will be subjected to polymerase chainreaction (PCR) to amplify the gene of interest and encode each copy withbarcode unique to the sample. Generally, PCR exponentially amplifies asingle or a few copies of a piece of DNA across several orders ofmagnitude, generating thousands to millions, or more, of copies of aparticular DNA sequence using a thermostable DNA polymerase. PCR will beused to amplify a portion of specific gene from the genome of themicrobes present in the sample. Any method that can amplify geneticmaterial quickly, accurately, and precisely can be used for librarypreparation.

The PCR primer will be designed carefully to meet the goals of thesequencing method. For instance, the PCR primer will contain a length ofnucleotides specific to the target gene, may contain an adapter thatwill allow the amplicon, also known as the PCR product, to bind and besequenced on a high-throughput sequencing platform, and additionalnucleotides to facilitate sequencing. The portion of the gene withadapters, barcode and necessary additional nucleotides is known as the“amplicon.” It being understood that future systems may not use, orneed, adaptors.

The microbial ribosome is made up component proteins and non-coding RNAmolecules, one of which is referred to as the 16S ribosomal RNA (or 16SrRNA). The 16S subunit is a component of the small subunit (SSU) ofbacterial and archaeal ribosomes. It is 1.542 kb (or 1542 nucleotides)or another specified length. The gene encoding the 163 subunit isreferred to as the 16S rRNA gene. The 16S rRNA gene is used forreconstructing phylogenies because it is highly conserved betweendifferent species of bacteria and archaea, meaning that is an essential(stable) part of the organisms who encode it in their genomes and it canbe easily identified in genomic sequences, but it additionally containsregions that are highly unique (but most likely changed incrementally)and are used for classification sake, in other words there is aphylogenetic signature in the sequence of the gene. As a result of thesesame properties, batch sequencing of all of the 16S rRNA gene sequencein a sample containing many microbial taxa are informative about whichmicrobial taxa are present. These studies are made possible by theremarkable observation that a small fragment of the 16S rRNA gene can besufficient as a proxy for the full-length genomic sequence for manymicrobial community analyses, including those based on a phylogenetictree.

Sequencing read accuracy and precision can affect the outcomes of anyanalysis including phylogenetic trees produced from those sequences.Some sequencing machines provide software that could be used to inferphylogenetic trees. For example, although the phylogenetic treesproduced from approximately 250-base reads from the 454 Life Sciences™(Roche) GS FLX instrument are relatively inaccurate, they are still muchbetter, as has been identified and is known to the art, than the “starphylogeny,” (phylogeny that assumes all species are equally related),that all non-phylogenetic methods for comparing communities useimplicitly (e.g.; by counting how many species are shared). However,such trees should, at most, be used as a guide to community comparisonsand not for inferring true phylogenetic relationships among reads.Advances in sequencing technology, such as the availability of 400-basereads with the Titanium™ kit from Roche; the Illumina™ platforms whichcan produce 450 Gb per day, and in the course of a 10.8 day run produces1.6 billion 100-base paired-end reads (HiSeq2000) or for single-dayexperiments can generate 1.5 Gb per day from 5 million 150-basepaired-end reads (MiSeq™), or in the future, the availability ofinstruments providing 1500-base single-molecule reads, as reported byPacific Biosciences™, will also improve the accuracy/productivity ofexisting methods for building phylogenetic trees and classifyingfunctions of metagenomic reads.

Although metagenomics and other alternative techniques provide insightinto all of the genes (and potentially gene functions and geneactivities) present in a given community, 16S rRNA-based studies areextremely valuable given that they can be used to discover and recordunexplored biodiversity and the ecological characteristics of eitherwhole communities or individual microbial taxa at an even lower relativecost. 16S rRNA phylogenies tend to correspond well to trends in overallgene content. Therefore the ability to relate trends at the specieslevel to host or environmental parameters has proven immensely powerfulto understanding the relationships between the microbes and the world.

Alternative microbiome measurement techniques provide importantinformation that is complementary to 16S rRNA or other marker-gene data:metagenomics provides genome content for the entire microbiome;transcriptomics measures gene expression by microbes, indicating whichgenes are actually being used by the microbes; proteomics measuresactual production of enzymes and other functional proteins in themicrobiome; metabolomics directly measures metabolite content in asample.

Generally, analysis of ribosomal genes either by themselves or incombination (SSU, LSU, ITS) will be used for the determination andcharacterization of microbes in industrial settings where the onlyrequirement for choosing the particular gene for amplification is thatthe gene is at least somewhat conserved between different species ofmicrobes. For instance, the amplification, sequencing and analysis ofthe small subunit (“SSU”) of the ribosomal gene (16S rRNA gene) would beused for bacteria and archaea while analysis of the eukarytotes such asnematodes, ciliates and amoeba would analyze the small subunit ribosomalgene (18S rRNA gene) common in these organisms. Further, LSU, ITS andthe mitochondrial marker such as Cytb or cox1, may also be used andcould provide enhanced performance. Fungal populations may also becharacterized by the intragenic transcribed spacer gene (“ITS gene”) inaddition to 18S rRNA gene. Furthermore, the large subunit ribosomal gene(“LSU”) could be analyzed alone or in combination with portions of theSSU in a single amplicon. The genetic material for any analysis could bederived from DNA or cDNA (i.e., complementary DNA) produced from thereverse transcription of RNA isolated from the target sample or samples.

Complete marker genes, such as the examples used above, generallycannot, because of their length, be sequenced using high-throughputmethods. However, the use of PacBio or Moleculo technologies can providethe ability to obtain such a complete sequence with high fidelity.Therefore, typically a shorter region of the marker gene sequence mustbe selected to act as proxy. Currently, there is no consensus on asingle best region, and consequently different groups are sequencingdifferent or multiple regions. This diversity of methods hinders directcomparisons among studies. Standardization on a single region would behelpful on this front. Of the nine variable regions in the 16S rRNAgene, several of the more popular regions include the regionssurrounding V2, V4, and V6. Generally, a combination of variable andmoderately conserved regions appears to be optimal for performinganalyses at different phylogenetic depths. Both the choice of region andthe design of the primers are crucial, and poor design of primers aswell as the use of different primers can lead to radically differentexperimental conclusions. Additionally, primer bias due to differentialannealing leads to the over- or underrepresentation of specific taxa canlead to some groups being missed entirely if they match the consensussequence poorly. Issues of primer bias can be important. For example,although some widely used primers such as 8F, 337F, 338R, 515F, 915F,930R, 1046R, and 1061R match >95% of the sequences in Ribosome DatabaseProject (RDP) from all of the major bacterial phyla in the normal humangut (Firmicutes, Bacteroidetes, Actinobacteria, Verrucomicrobia, andProteobacteria), others miss specific divisions. For example, 784F isbiased against Verrucomicrobia; 967F matches <5% of Bacteroidetes; and1492R matches 61% of Actinobacteria, 54% of Proteobacteria, and fewerthan half of the other divisions. Comparisons of relative abundanceamong different studies should thus be treated with caution. However,meta-analyses of presence/absence data from different studies isparticularly useful for revealing broad trends, even when differentstudies use different primers.

As more sequence data and better taxonomic assignments become available,improved primer sets, with better coverage (including primers forarchaea and eukaryotes), will likely provide a substantial advantageover present degenerate primer techniques (where a mixture of differentprimers that allow variation at one or more nucleotide in the sequence).Specifically, 16S rRNA and 18s rRNA reads from metagenomic studiesprovide a source of sequences that is not subject to PCR primer bias(although other biases are present) and therefore covers taxa that aremissed by existing but popular primer sets, although in practiceexploiting this information has been quite challenging. Anotherpromising approach is the use of miniprimers, which, together with anengineered DNA polymerase, may allow greater coverage of desired groups.Likewise nested PCR techniques could be used for example, and notlimited to identify specific motifs, sequences, genes, organisms, and/orany combination of these.

Furthermore, improvements in the ability to produce high quantities ofprimers (e.g. millions of individual primers) and appropriate reactionconditions will enable amplification of high quantities of regions (e.g.millions of individual regions), which may be distinct to each microbeor targeted at multiple sites obtained from existing databases or fromshotgun sequencing. Such an application could be used to improveddiscrimination and/or prediction for a particular environment and targetparameter (e.g. oil saturation in a reservoir) For example, we mightdetermine that a collection of genes related to hydrocarbon reduction oroxidation are predictive of oil/water saturation, and then design primersets against all of such genes identified via shotgun sequencing of aseries of samples obtained from wells with varying oil/water saturationlevels. Likewise, it might also be possible to design a chip on whichprimers and/or partial gene sequences could be based and amplify thosegenes of interest.

The primers designed for amplification will be well-suited for thephylogenetic analysis of sequencing reads. Thus, the primer design willbe based on the system of sequencing, e.g., chain termination (Sanger)sequencing or high-throughput sequencing. Within the system, there arealso many options on the method. For example, for high-throughputsequencing, the sequencing can be performed by, but is not limited to,454 Life Sciences™ Genome Sequencer FLX (Roche) machine or the Illumina™platforms (MiSeq™ or HiSeq™). These will be described more in theSequencing section below.

Barcoding

High-throughput sequencing, described below, has revolutionized manysequencing efforts, including studies of microbial community diversity.High-throughput sequencing is advantageous because it eliminates thelabor-intensive step of producing clone libraries and generates hundredsof thousands of sequences in a single run. However, two primary factorslimit culture-independent marker gene-based analysis of microbialcommunity diversity through high-throughput sequencing: 1) eachindividual run is high in cost, and 2) separating samples from a singleplate across multiple runs is difficult. For example, analysis ofmultiple libraries on the 454™/Roche sequencers has room for up to amaximum of only 16 independent samples, which have to be physicallysegregated using manifolds on the sequencing medium. These separationmanifolds block wells on the sequencing plate from accommodatingbead-bound DNA template molecules, and thus limit the number of outputsequences.

A solution to these limitations is barcoding. For barcoding, a uniquetag will be added to each primer(s) before PCR amplification. Becauseeach sample will be amplified with a known tagged (barcoded) primer(s),an equimolar mixture of PCR-amplified DNA can be sequenced from eachsample and sequences can be assigned back to samples based on theseunique barcodes. The presence of these assigned barcodes allow forindependent samples to be combined for sequencing, with subsequentbioinformatic separation of the sequencer output. By not relying onphysical separators, this procedure maximizes sequence space andmultiplexing capabilities. This technique will be used to process manysamples (eg 25, 200, 1000, and above) and is mostly only limited by thenumber of barcoded primers used and the desired coverage (due to thetotal sequences expected from the given machine or method, and thereagents and/or cycles possible for the given machine used insequencing) in a single high-throughput sequencing run. This number willbe increased depending on advances in high-throughput sequencingtechnology, without limit to the number of samples to be sequenced in asingle high-throughput sequencing run.

Barcodes, or unique DNA sequence identifiers, have traditionally beenused in different experimental contexts, such as sequence-taggedmutagenesis (STM) screens where a sequence barcode acts as an identifieror type specifier in a heterogeneous cell-pool or organism-pool.However, STM barcodes are usually 20-60 bases (or nucleotides, nt) long,are pre-selected or follow ambiguity codes, and exist as one unit orsplit into pairs. Such long barcodes are not particularly compatiblewith available high-throughput sequencing platforms because ofrestrictions on read length.

Although very short (2- or 4-nt) barcodes can be used withhigh-throughput sequencing platforms, a more definitive assignment ofsamples and/or for enhanced multiplexing capabilities can beaccomplished by lengthening the barcodes or variations in the fixedforward and reverse linkers used to generate the initial cDNA libraries.Shorter barcodes also have a steeper trade-off between number ofpossible barcodes and the minimum number of nucleotide variationsbetween individual barcodes.

Existing barcoding methods have limits both in the number of uniquebarcodes used and in their ability to detect sequencing errors thatchange sample assignments (this robustness is especially important forsample assignment because the 5′ end of the read (sequence for onestrand of nucleic acid in a sample) is somewhat more error-prone).Barcodes based on error-correcting codes, which are widely used indevices in other technologies like telecommunications and electronics,will be applied for high-throughput sequencing barcoding purposes.

For example, a class of error-correcting codes called Hamming codes,which use a minimum amount of redundancy and will be simple to implementusing standard linear algebra techniques. Hamming codes, like allerror-correcting codes, employ the principle of redundancy and addredundant parity bits to transmit data over a noisy medium. Sampleidentifiers will be encoded with redundant parity bits. Then the sampleidentifiers will be “transmitted” as codewords. Each base (A, T, G, C)will be encoded using 2 bits and using 8 bases for each codeword.Therefore, 16-bit codewords will be transmitted. The codeword and basesis not limited to these numbers, as any number of bits and codewords canbe designed by a person of ordinary skill in the art. The design of thebarcode is based on the goals of the method. Hamming codes are unique inthat they use only a subset of the possible codewords, particularlythose that lie at the center of multidimensional spheres (hyperspheres)in a binary subspace. Single bit errors fall within hyperspheresassociated with each codeword, and thus they can be corrected. Doublebit errors do not fall within hyperspheres associated with eachcodeword, and thus they can be detected but not corrected.

Other encoding schemes, such as Golay codes, will also be used forbarcoding. Golay codes of 12 bases can correct all triple-bit errors anddetect all quadruple-bit errors. The extended binary Golay code encodes12 bits of data in a 24-bit word in such a way that any 3-bit errors canbe corrected or any 7-bit errors can be detected. The perfect binaryGolay code, has codewords of length 23 and is obtained from the extendedbinary Golay code by deleting one coordinate position (conversely, theextended binary Golay code is obtained from the perfect binary Golaycode by adding a parity bit). In standard code notation the codes haveparameters corresponding to the length of the codewords, the dimensionof the code, and the minimum Hamming distance between two codewords,respectively.

In mathematical terms, the extended binary Golay code consists of a12-dimensional subspace W of the space V=F₂ ²⁴ of 24-bit words such thatany two distinct elements of W differ in at least eight coordinates.Equivalently, any non-zero element of W has at least eight non-zerocoordinates. The possible sets of non-zero coordinates as w ranges overW are called codewords. In the extended binary Golay code, all codewords have the Hamming weights of 0, 8, 12, 16, or 24. Up to relabelingcoordinates, W is unique.

FIG. 6 shows an example of the general design for barcoded primers forhigh-throughput sequencing. The primer will be designed to includenucleotides specific for the sequencing platform 601; nucleotidesspecific for the gene of interest 602; nucleotides for the Golay barcode603; and the nucleotides of the gene 604. Upon amplification, onecontiguous string of nucleotides known as the “forward” primer 605 willbe formed from the platform specific sequencing adaptors 301 and thegene specific primer and linker 602. Additionally formed uponamplification will be one contiguous string of nucleotides known as the“reverse” primer formed from the platform specific sequencing adaptors601, the gene specific primer and linker 602, and the barcode 603.

FIG. 7 shows the general scheme for PCR using barcoded primers, designedas previously described. Double stranded target DNA 706 is denatured707. Strands 701 and 702 will be annealed to the gene via the genespecific primer and linker (FIG. 6, 602). Thermostable DNA polymeraseextends primers creating strands 703 and 704. Strands 703 and 704 willbe denatured from the target DNA. Then strand 701 will be annealed tostrand 704 while strand 702 will be annealed to strand 703. Throughamplification, new strands 705 are produced. Strand 705 is a barcodedamplicon that can be sequenced. Further, other error-correcting codesmay be utilized such as Gray codes, low-density parity check codes, etc.

The technique of high-throughput sequencing of these barcoded ampliconsyields a robust description of the changes in bacterial communitystructure across the sample set. A high-throughput sequencing run isexpensive, and the large number of custom primers required only adds tothis cost. However, the barcoding technique allows for thousands ofsamples to be analyzed simultaneously, with each community analyzed inconsiderable detail. Although the phylogenetic structure and compositionof the surveyed communities can be determined with a high degree ofaccuracy, the barcoded high-throughput sequencing method may not allowfor the identification of bacterial taxa at the finest levels oftaxonomic resolution. However, with increasing read lengths insequencing, this constraint will gradually become less relevant.

Example 6

In one example, specifically for the Illumina™ sequencing machinery(described below), the following primers will be designed foramplification of 16S rRNA. The primer sequences in this protocol arealways listed in the 5′→3′ orientation.

515f PCR Primer Sequence—Forward primer

Field description (space-delimited):

1. 5′ Illumina™ adapter

2. Forward primer pad

3. Forward primer linker

4. Forward primer (515f)

(SEQ ID NO: 1) AATGA TACGG CGACC ACCGA GATCT ACACT ATGGTAATTG TGTGC CAGCM GCCGC GGT AA

806r PCR primer sequence—Reverse primer, barcoded

Sheet of primer constructs contains 2168 Golay barcoded reverse PCRprimers generated specifically for this set of primers.

Field description (space-delimited):

1. Reverse complement of 3′ Illumina™ adapter

2. Golay barcode

3. Reverse primer pad

4. Reverse primer linker

5. Reverse primer (806r)

(SEQ ID NO: 2) CAAGC AGAAG ACGGC ATACG AGAT XXXXXXXXXXXXAGTCA GTGAG CCGGA CTACH VGGGT WTCTA AT

Illumina™ PCR Conditions: 515f-806r region of the 16S rRNA gene:

Complete reagent recipe (master mix) for IX PCR reaction

PCR Grade H2O (note a) 13.0 μL 5 Primer Hot MM (note b) 10.0 μL Forwardprimer (10 μM)  0.5 μL Reverse primer (10 μM)  0.5 μL Template DNA  1.0μL Total reaction volume 25.0 μL Notes: PCR grade water was purchasedfrom MoBio ™ Laboratories Five Prime Hot Master Mix (5 prime) Finalprimer concentration of mastermix: 0.2 μM

Thermocycler Conditions for 96 well thermocyclers:

94° C. 3 minutes

94° C. 45 seconds

50° C. 60 seconds

72° C. 90 seconds

Repeat steps 2-4 35 times

72° C. 10 minutes

4° C. HOLD

Thermocycler Conditions for 384 well thermocycler

94° C. 3 minutes

94° C. 60 seconds

50° C. 60 seconds

72° C. 105 seconds

Repeat steps 2-4 35 times

72° C. 10 minutes

4° C. HOLD

The samples will be amplified in triplicate, meaning each sample will beamplified in 3 replicate 25 μL PCR reactions (or the number ofreplicated required to meet an efficient and valid yield of DNA). Thetriplicate (or more as is deemed necessary) PCR reactions will becombined for each sample into a single volume. The combination willresult in a total of 75 μL of amplicon for each sample. The ampliconsfrom different samples will not be combined at this point. The ampliconsfor each sample will be run on an agarose gel. Expected band size for515f/806r is roughly 300-350 bp. Amplicons will be quantified usingPicogreen's® instructions or another sensitive DNA assessment methodsuch as, Qubit® assays could be used. An equal amount of amplicon fromeach sample will be combined into a single, sterile tube. Generally, 240ng of DNA per sample will be pooled. However, higher amounts can be usedif the final pool will be gel isolated or when working with low biomasssamples. When working with multiple plates of samples, it is typical toproduce a single tube of amplicons for each plate of samples. Theamplicon pool will be cleaned using MoBio™ UltraClean® PCR Clean-Up Kit#12500, following the instructions provided therein. If working withmore than 96 samples, the pool will need to be split evenly for cleaningand then recombined. If spurious bands are present on the previouslymentioned agarose gel, half of the final pool will be run on a gel andthen gel extracted to select only the target bands. The concentration ofthe final pool will be determined fluormetrically with PicoGreen® ds DNAreagent, or equivalent assay, as spectrophotometric methods are notsuitable for quantification. However, the 260 nm/280 nm ratio should bedetermined spectrophotometrically as this is a measure of sample purityand can be critical to successful sequencing with the ratio between 1.8and 2.0. Negative or blank controls of all reagents should be includedto test for contamination. An aliquot of this final sample will be usedfor sequencing along with sequencing primers listed below.

Read 1 sequencing primer:

Field description (space-delimited):

1, Forward primer pad

2, Forward primer linker

3, Forward primer

(SEQ ID NO: 3) TATGG T AA TT GTGTG CCAGC MGCCG CGGTA A

Read 2 sequencing primer:

Field description (space-delimited):

1, Reverse primer pad

2, Reverse primer linker

3, Reverse primer

(SEQ ID NO: 4) AGTCA GTCAG CCGGA CTACH VGGGT WTCTA AT

Index sequence primer:

Field description (space-delimited):

1. Reverse complement of reverse primer

2. Reverse complement of reverse primer linker

3. Reverse complement of reverse primer pad

(SEQ ID NO: 5) ATTAG AWACC CBDGT AGTCC GGCTG ACTGA CT

Example 7

In another example, for each sample, the 16S rRNA gene will be amplifiedusing a primer set including:

Forward Primer

(5′GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG-3′; SEQ ID NO: 6) whichcontains the 454 Life Science™ primer B, the broadly conserved bacterialprimer 27F, and a 2-base linker sequence (“TC”);

Reverse Primer

5′GCCTCCCTCGCGCCATCAGNNNNNNNNNNNNCATGCTGCCTCCCGTAGGA-3′; SEQ ID NO:7)which contains the 454 Life Sciences™ primer A, the bacterial primer338R, a “CA” inserted as a linker between the barcode and the rRNAprimer (with the specific linker depending on the region of sequencetargeted by the primer and which, unlike the PCR primer which isdesigned to be complimentary to the target sequences, is specificallydesigned to not be complimentary to the target sequences so the basepairing interactions are disrupted in all target sequences at thisposition—if this linker were not present, some barcodes would anneal tothe target, while some would not, leading to barcode-specific PCRbiases) and a unique 12-bp error-correcting Golay barcode used to tageach PCR product (designated by NNNNNNNNNNNN). PCBs will consist of 0.25(30 μm) of each forward and reverse primer, 3 μL of template DNA, and22.5 μL of Platinum® PCR SuperMix by Invitrogen™. Samples will bedenatured at 94° C. for 3 min, then amplified by using 35 cycles of 94DC for 45 seconds, 50° C. for 30 seconds, and 72° C. for 90 seconds. Afinal extension of 10 minutes at 72° C. will be added at the end of theprogram to ensure complete amplification of the target region. Allsamples will be amplified in triplicate. Although, PCR should beoptimized for the specific reaction. Negative controls (both no-templateand template from unused cotton swabs (referring back to Example 6))will be included in all steps of the process to check for primer orsample DNA contamination. All aliquoting and diluting of primers, aswell as assembly of PCRs, will be done in a PCR hood in which allsurfaces and pipettes had been decontaminated with DNA AWAY™ byMolecular BioProducts™ and exposed to UV light for 30 minutes.

A composite sample for DNA sequencing will be prepared by poolingapproximately equal amounts of PCR amplicons from each sample. Thereplicate PCRs for each sample will be combined and cleaned with theMobio™ UltraCleane-htp PCR Clean-up kit as directed by the manufacturer.Each sample (3 μL) was then quantified by using PicoGreen® dsDNA reagentby Invitrogen™ in 1×Tris-EDTA (pH 8.2) in a total volume of 200 L onblack, 96-well microtiter plates on a BioTek™ Synergy™ HTP microplatereader by BioTek Instruments, using the 480/520-nm excitation andemission filter pair. Once quantified, the appropriate volume of thecleaned PCR amplicons will be combined in a sterile, 50-mL polypropylenetube and precipitated on ice with sterile 5 M NaCl (0.2 M finalconcentration) and 2 volumes of ice-cold 100% ethanol for 45 minutes.The precipitated DNA will be centrifuged at 7,800 g for 40 minutes at 4°C., and the resulting will be washed with an equal volume of 70% ethanoland will be centrifuged again at 7,800 g for 20 minutes at 4° C. Thesupernatant will be removed, and the pellet will be air-dried for 7minutes at room temperature, then resuspended in 100 μL of DNA-nucleasefree water. The sample will be then ready for sequencing.

Example 8

Small-subunit ribosomal genes (16S) will be amplified using universal515F (5′-GTGCCAGCMGCCGCGGTAA-3′; SEQ ID NO:8) and 1391R(5′GACGGGCGGTGWGTRCA-3′) primers for bacterial 16S rRNA genes. The PCRreaction will contained 1×PCR Buffer from Invitrogen, 2.5 mM MgCl2, 0.2μM of each primer, 0.2 μM dNTPs, 0.5 U Taq DNA polymerase by Invitrogen™and 1.0 μl template DNA. Amplification will be accomplished by initialdenaturation at 94° C. for 3 minutes followed by 25 cycles of 94° C. for30 seconds, 50° C. for 30 seconds and 72° C. for 30 seconds with a finalextension at 72° C. for 10 minutes. Each DNA sample will be amplified intriplicate and the amplicons will be pooled by plot and run on a 1.5%agarose gel. The bands will be purified using the Promega™ Wizard® SVGel and PCR Clean-Up System. The sample will be then ready forsequencing.

Example 9

In another example, a portion of the 16S small-subunit ribosomal gene(positions 27 to 338 [V1 and V2]; Escherichia coli numbering) will beamplified using a 27F primer with a Roche 454™ A pyrosequencing adapter,while the 338R primer will contain a 12-bp bar-code sequence, a TClinker, and a Roche 454™ B sequencing adapter. The particular generegion has been shown to be very appropriate for accurate taxonomicclassification of bacterial sequences, because other regions of the 16SrRNA gene can lead to significant misclassification of sequences. Thebarcode for each sample will be unique and error correcting tofacilitate sorting of sequences from a single pyrosequencing run. PCRswill be conducted with 30 μM of each forward and reverse primer, 1.5 μltemplate DNA, and 22.5 μl Platinum® PCR SuperMix by Invitrogen™. Eachsample will be amplified in triplicate, pooled, and cleaned using aMoBio™ 96 htp PCR cleanup kit. Equal amounts of PCR product for eachsample will be combined in a single tube for sequencing.

Sequencing

The vast majority of life on earth is microbial, and the vast majorityof these microbial species has not been, and is not capable of beingeasily cultured in the laboratory. Consequently, our primary source ofinformation about most microbial species consists of fragments of theirDNA sequences. Sequencing a DNA library will be done on a platformcapable of producing many sequences for each sample contained in thelibrary. High-throughput sequencing technologies have allowed for newhorizons in microbial community analysis by providing a cost-effectivemethod of identifying the microbial OTUs that are present in samples.These studies have drastically changed our understanding of themicrobial communities in the human body and on the planet. Thisdevelopment in sequencing technology, combined with more advancedcomputational tools that employ metadata to relate hundreds of samplesto one another in ways that reveal clear biological patterns, hasreinvigorated studies of the 16S rRNA and other marker genes. Studies of16S rRNA genes provide a view of which microbial taxa are present in agiven sample because these genes provide an excellent phylogeneticmarker. Although alternative techniques, such as metagenomics, provideinsight into all of the genes (and potentially gene functions) presentin a given community, 16S rRNA-based surveys are extraordinarilyvaluable given that they can be used to document unexplored biodiversityand the ecological characteristics of either whole communities orindividual microbial taxa. Perhaps because 16S rRNA phylogenies tend tocorrespond well to trends in overall gene content, the ability to relatetrends at the species level to host or environmental parameters hasproven immensely powerful. The DNA encoding the 16S rRNA gene has beenwidely used to specify bacterial and archaeal taxa, since the region canbe amplified using PCR primers that bind to conserved sites in most orall species, and large databases are available relating 16S rRNAsequences to correct phylogenies. However, as previously discussed,other genes or regions can be used to specify the taxa, such as 18S,LSU, ITS, and SSU (e.g., 16S). For the purposes of bacteria, cpn60 orftsZ, or other markers, may also be utilized.

New technologies have led to extraordinary decreases in sequencingcosts. This rapid increase in sequencing capacity has led to a processin which newer sequencing platforms generate datasets of unprecedentedscale that break existing software tools: new software is then developedthat exploits these massive datasets to produce new biological insight,but in turn the availability of these software tools prompts newexperiments that could not previously have been considered, which leadto the production of the next generation of datasets, starting theprocess again.

High-Throughput Sequencing

With the advent of high-throughput sequencing, characterization of thenucleic acid world is proceeding at an accelerated pace. Three majorhigh-throughput sequencing platforms are in use today: 1) the GenomeSequencers from Roche/454 Life Sciences™ [GS-20 or GS-FLX]; 2) the 1GAnalyzer from Illumina™/Solexa™ which includes the MiSeq™ and theHiSeq™; and 3) the SOLiD™ System from Applied Biosystems™. Comparisonacross the three platforms reveals a trade-off between average sequenceread length and the number of DNA molecules that are sequenced. TheIllumina™/Solexa™ and SOLiD systems provide many more sequence reads,but render much shorter read lengths than the 454™/Roche GenomeSequencers. This makes the 454™/Roche platform appealing for use withbarcoding technology, as the enhanced read length facilitates theunambiguous identification of both complex barcodes and sequences ofinterest. However, even reads of less than 100 bases can be used toclassify the particular microbe in phylogenetic analysis. Any platform,for example, Illumina™, providing many reads and read lengths of apredetermined necessary length, for example, 150 base pairs or 100 basepairs, is acceptable for this method.

Because the accuracy of phylogenetic reconstruction depends sensitivelyon the number of informative sites, and tends to be much worse below afew hundred base pairs, the short sequence reads produced fromhigh-throughput sequencing, which are 100 base pairs on average for theGS 20 (Genome Sequencer 20 DNA Sequencing System, 454 Life Sciences™),may be unsuitable for performing phylogenetically based communityanalysis. However, this limitation can be at least partially overcome byusing a reference tree based on full-length sequences, such as the treefrom the Greengenes 16S rRNA ARB Database, and then using an algorithmsuch as parsimony insertion to add the short sequence reads to thisreference tree. These procedures are necessarily approximate, and maylead to errors in phylogenetic reconstruction that could affect laterconclusions about which communities are more similar or different. Onesubstantial concern is that because different regions of the rRNAsequence differ in variability, conclusions drawn about the similaritiesbetween communities from different studies might be affected more by theregion of the 16S rRNA that was chosen for sequencing than by theunderlying biological reality.

The increase in number of sequences per run from parallelhigh-throughput sequencing technologies such as the Roche 454 GS FLX™(5×105) to IIlumina GAIIx™ (1×108) is on the order of 1,000-fold andgreater than the increase in the number of sequences per run from Sanger(1×103 through 1×104) to 454™. The transition from Sanger sequencing to454™ sequencing has opened new frontiers in microbial community analysisby making it possible to collect hundreds of thousands of sequencesspanning hundreds of samples. A transition to the Illumina™ platformallows for more extensive sequencing than has previously been feasible,with the possibility of detecting even OTUs that are very rare. By usinga variant of the barcoding strategy used for 454™ with the Illumina™platform, thousands of samples could be analyzed in a single run, witheach of the samples analyzed in unprecedented depth.

A few sequencing runs using 454™/Roche's pyrosequencing platform cangenerate sufficient coverage, among many other applications, forassembling entire microbial genomes, for the discovery, identificationand quantitation of small RNAs, and for the detection of rare variationsin cancers, among many other applications. However, as the analyticaltechnology becomes more advanced, the coverage provided by this systembecomes unnecessary for phylogenetic classification. For analysis ofmultiple libraries, the 454/Roche™ pyrosequencers can accommodate amaximum of only 16 independent samples, which have to be physicallyseparated using manifolds on the sequencing medium, drastically limitingthe utility in the effort to elucidate the diverse microbial communitiesin each sample. Relatively speaking, the Illumina™ platforms areexperiencing the most growth. However, with the constant improvements insequencing systems, the different platforms that will be used willchange over time. Generally, the method describe herein will be usedwith any available high-throughput sequencing platform currentlyavailable or will be available in the future. For example, the methoddescribed herein will be applied to a sequencing method wherein thegenetic material will be sequenced without barcoding by simply placingthe DNA or RNA directly into a sequencing machine.

In general, high-throughput sequencing technology allows for thecharacterization of microbial communities orders of magnitude faster andmore cheaply than has previously been possible. For example, a typicalIllumina MiSeq™ run can produce as many as 50 million, short paired endreads in the v3 chemistry (˜300 by long; 1.5×10⁹ bp of data, or in thev2 chemistry, 250 bp; 7.5×10⁹ bp) in 65 hours compared to Sangersequencing which may take a day or more to produce only 96 reads of 800bp in length (˜7.7×10⁴ bp of data). In addition, the ability to barcodeamplicons from individual samples means that hundreds of samples can besequenced in parallel, further reducing costs and increasing the numberof samples that can be analyzed. Though high-throughput sequencing readstend to be short compared to those produced by the Sanger method, thesequencing effort is best focused on gathering more short sequences(less than 150 base pairs or less than 100 base pairs) rather than fewerlonger ones as much of the diversity of microbial communities lieswithin the “rare biosphere,” also known as the “long tail,” thattraditional culturing and sequencing technologies are slow to detect dueto the limited amount of data generated from these techniques.

In statistics, a power law is a functional relationship between twoquantities, where one quantity varies as a power of another. Power lawdistributions or functions characterize an important number of behaviorsfrom nature and human endeavor. The observation of such a distributionoften points to specific kinds of mechanisms, and can often indicate adeep connection with other, seemingly unrelated systems. An example of apower law graph is shown in FIG. 15.

FIG. 15 is a graph of a power law distribution. Each line, e.g., 1501,1502, represents one of 134 human gut microbiome samples from healthyadults living in the USA included in a global survey of gut microbialdiversity. To avoid undersampling of the rare microbiome, samples weresequenced at very high depth, ranging from 305,631 to 3,486,888sequences per sample (mean±s.d.=2,018,984±543,962.2). The x- and y-axesare log scale (i.e., it is a log-log plot), where the y value representsthe abundance of an OTU, and the x is the “rank” of that OTU from mostabundant to least abundant. The fact that this relationship is linear ina log-log plot defines it as embodying a power law distribution. Thismeans that the most abundant OTU is 10 times more abundant than thetenth most abundant OTU.

In the power law graph example, a long tail of some distributions ofnumbers is the portion of the distribution having a large number ofoccurrences far from the “head” central part of the distribution. Thedistribution could involve many factors including but not limited topopularities, random numbers of occurrences of events with variousprobabilities, etc. A probability distribution is said to have a longtail, if a larger share of population rests within its tail than wouldunder a normal distribution. A long-tail distribution will arise withthe inclusion of many values are unusually far from the mean. Along-tailed distribution is a particular type of heavy-taileddistribution.

Microorganisms of extremely low abundance have been designated the “rarebiosphere” or “long tail.” The ecological significance of raremicroorganisms is just beginning to be understood. One hypothesis isthat rare members represent a dormant seed bank. Members of this seedbank may become active at random or in direct response to changes in theenvironment, for instance, to initiate community recovery afterdisturbance. This hypothesis is supported by a recent investigation ofmarine bacterioplankton responses to organic carbon additions, whereinrare members increased in abundance from less than 10 sequences to asmany as thousands after carbon amendment. Similarly, a study in theWestern English Channel showed that community members in low abundancewere persistent over time, and that, in a few cases, populations of raremembers occasionally bloomed. However, there also are situations inwhich rare members are hypothesized to be less important for thecommunity, such as when populations are becoming extinct or are betweenfavorable environments. Because members of the rare biosphere mayprovide novel products and processes, bioprospecting for these organismshas been made a priority.

The length of the read of a sequence describes the number of nucleotidesin a row that the sequencer is able to obtain in one read. This lengthcan determine the type of taxa classification (e.g., family, genus orspecies) or OTU obtained. For example, a read length of approximately300 base pairs will probably provide family information, but perhaps nota species determination. Depth of coverage in DNA sequencing refers tothe number of times a nucleotide is read during the sequencing process.On a genome basis, it means that, on average, each base has beensequenced a certain number of times (10×, 20× . . . ). For a specificnucleotide, it represents the number of sequences that added informationabout that nucleotide. Coverage is the average number of readsrepresenting a given nucleotide in the reconstructed sequence. Depth canbe calculated from the length of the original genome (G), the number ofreads (N), and the average read length (L) as N×L/G. For example, ahypothetical genome with 2,000 base pairs reconstructed from 8 readswith an average length of 500 nucleotides will have 2× redundancy. Thisparameter also enables estimation of other quantities, such as thepercentage of the genome covered by reads (coverage). Sometimes adistinction is made between sequence coverage and physical coverage.Sequence coverage is the average number of times a base is read.Physical coverage is the average number of times a base is read orspanned by mate paired reads.

The line 801 plotted in the graph of FIG. 8 shows the ranked abundanceof the OTUs on the x-axis with the most abundant species near the originof the plot. The y-axis is the relative abundance of the OTU. The rarebiosphere is the part of the line which has low values on the Y-axis.For instance, OTU 10 is the 10^(th) most abundant organism butrepresents less than 0.1% of the total OTUs present in the sample, whileOTU 1 represents 50% of the OTUs in the same sample. Organisms of lowerabundance rank can be detected if more sequence reads are collected. Forexample, the most abundant OTUs that are in box 802 are verified by arelatively low read depth. The moderately abundant OTUs that are in box803 are verified by an increasing read depth. The long tail, whichsignifies the rare members of the community, is in box 804. To verifythat these sequences are present, a higher read depth (i.e. moresequences) must be obtained. Analyzing the rare biosphere is attainablebecause sequencing depth provided by high-throughput sequencing allowsfor the detection of microbes that would otherwise be detected onlyoccasionally by chance with traditional techniques.

With existing technology, the realistic time requirement for nucleicacid extraction, library preparation and sequencing is approximately afew days for a few samples. Analysis of the sequencing data will requirean additional few hours depending on the system and amount of sequencingdata produced. However, with minimizing the necessary read length, forexample, to less than 150 base pairs or less than 100 base pairs, andmaximizing the read depth in order to capture the organisms in the longtail of the power law graph, this time can be variable. Another variablefactor is the advances in technology for high-throughput sequencing.Thus high-throughput sequencing will allow for the analysis of the morerare members (low abundance organisms) of any environment which may playcritical role in, for example, oil and gas production, petroleumpipeline maintenance, food production, agriculture and other industrieswhere microbes are present within a time-frame feasible for industrialsettings. For example, the time from sampling to analysis of thesequencing information will be reduced to a few days or a few hours, andin another example, as quickly as under an hour, or under a few minutes,or preferably under a minute.

Pyrosequencing

One type of high-throughput sequencing is known as pyrosequencing.Pyrosequencing, based on the “sequencing by synthesis” principle, is amethod of DNA sequencing widely used in microbial sequencing studies.Pyrosequencing involves taking a single strand of the DNA to besequenced and then synthesizing its complementary strand enzymatically.The pyrosequencing method is based on observing the activity of DNApolymerase, which is a DNA synthesizing enzyme, with anotherchemiluminescent enzyme. The single stranded DNA template is hybridizedto a sequencing primer and incubated with the enzymes DNA polymerase,ATP sulfurylase, luciferase and apyrase, and with the substratesadenosine 5′ phosphosulfate (APS) and luciferin. Synthesis of thecomplementary strand along the template DNA allows for sequencing of asingle strand of DNA, one base pair at a time, by the detection of whichbase was actually added at each step.

The template DNA is immobile, and solutions of A, C, G, and Tnucleotides are sequentially added and removed from the reaction. Thetemplates for pyrosequencing can be made both by solid phase templatepreparation (streptavidin-coated magnetic beads) and enzymatic templatepreparation (apyrase-Fexonuclease). Specifically, the addition of one ofthe four deoxynucleoside triphosphates (dNTPs) (dATPaS, which is not asubstrate for a luciferase, is added instead of dATP) initiates the nextstep. DNA polymerase incorporates the correct, complementary dNTPs ontothe template. This base incorporation releases pyrophosphate (PPi)stoichiometrically. Then, ATP sulfurylase quantitatively converts PPi toATP in the presence of adenosine 5′ phosphosulfate. This ATP acts tocatalyze the luciferase-mediated conversion of luciferin to oxyluciferinthat generates visible light in amounts that are proportional to theamount of ATP. Light is produced only when the nucleotide solutioncomplements the particular unpaired base of the template. The lightoutput in the luciferase-catalyzed reaction is detected by a camera andanalyzed in a program. The sequence of solutions which producechemiluminescent signals allows the sequence determination of thetemplate. Unincorporated nucleotides and ATP are degraded by theapyrase, and the reaction can restart with another nucleotide.

IIlumina's™ Sequencing by Synthesis (SBS)

Illumina's™ sequencing by synthesis (SBS) technology with TruSeqtechnology supports massively parallel sequencing using a proprietaryreversible terminator-based method that enables detection of singlebases as they are incorporated into growing DNA strands.

A fluorescently labeled terminator is imaged as each dNTP is added andthen cleaved to allow incorporation of the next base. Since all fourreversible terminator-bound dNTPs are present during each sequencingcycle, natural competition minimizes incorporation bias. The end resultis true base-by-base. Although this is similar to pyrosequencing, thedifferences between the platforms are noteworthy. The method describedherein can be applied to any high-throughput sequencing technology,past, present or future. Pyrosequencing and SBS are merely examples anddo not limit the application of the method in terms of sequencing.

Facilities with basic laboratory capabilities could be modified for usein microbial community analysis. Having an on-site sequencing capabilitywill lower the amount of time from sample collection to data analysisand the production of useful results in a timely manner. Shortening thedistance from sample collection to sequencing will alleviate the needfor long-term preservation of the sample as well as diminishing thechances of losing samples. Sequencing can be performed on site when oiland gas fields are located in areas that lack the deliveryinfrastructure commonly available in many populated areas including buthave basic lab capabilities: remote areas lacking well maintained roads,easy access to airports or landing strips, off-shore locations, drillingfrom vessels based platforms, or the presence of any other physicalbarriers that necessitate long transit times from the well to the lab.

Analysis of Sequencing Data

Generally, as the expense of sequencing decreases, the methods forcomparing different communities based on the sequences they containbecome increasingly important, and are often the bottleneck in obtaininginsight from the data. Sequence data can be analyzed in a manner inwhich sequences are identified and labeled as being from a specificsample using the unique barcode introduced during library preparation,if barcodes are used, or sample identifiers will be associated with eachrun directly if barcodes are not used. Once sequences have beenidentified as belonging to a specific sample, the relationship betweeneach pair of samples will be determined based on the distance betweenthe collections of microbes present in each sample. In particular,techniques that allow for the comparison of many microbial samples interms of the phylogeny of the microbes that live in them (“phylogenetictechniques”) are often necessary. Such methods are particularly valuableas the gradients that affect microbial distribution are analyzed, andwhere there is a need to characterize many communities in an efficientand cost-effective fashion. Gradients of interest include differentphysical or chemical gradients in natural environments, such astemperature or nutrient gradients in certain industrial settings.

When comparing microbial communities, researchers often begin bydetermining whether groups of similar community types are significantlydifferent. However, to gain a broad understanding of how and whycommunities differ, it is essential to move beyond pairwise significancetests. For example, determining whether differences between communitiesstem primarily from particular lineages of the phylogenetic tree, orwhether there are environmental factors (such as temperature, salinity,or acidity) that group multiple communities together is pivotal to ananalysis. The analysis systems described herein are merely examples andare not limiting. Any methods which will distill massive data sets fromraw sequences to human-interpretable formats, for example, 2-D or 3-Dordination plots, supervised learning for predictive modeling, or moretraditional statistical significance testing, allowing for patternelucidation and recognition, will be used.

QIIME

After DNA sequence data is obtained the bioinformatics stages begin.This includes barcode decoding (demultiplexing), sequence qualitycontrol, “upstream” analysis steps (including clustering of closelyrelated sequences and phylogenetic tree construction), and “downstream”diversity analyses, visualization, and statistics. All of these stepsare currently facilitated by the Quantitative Insights Into MicrobialEcology (QIIME, www.qiime.org) open source software package, which isthe most widely used software for the analysis of microbial communitydata generated on high-throughput sequencing platforms. QIIME wasinitially designed to support the analysis of marker gene sequence data,but is also generally applicable to “comparative-omics” data (includingbut not limited to metabolomics, metatranscriptomics, and comparativehuman genomics).

QIIME is designed to take users from raw sequencing data (for example,as generated on the IIlumina™ and 454™ platforms) though the processingsteps mentioned above, leading to quality statistics and visualizationsused for interpretation of the data. Because QIIME scales to billions ofsequences and runs on systems ranging from laptops to high-performancecomputer clusters, it will continue to keep pace with advances insequencing technologies to facilitate characterization of microbialcommunity patterns ranging from normal variations to pathologicaldisturbances in many human, animal and environmental ecosystems.

For microbiome data analysis, the following steps will be taken. Unlessotherwise noted, the steps will be performed with QIIME. However, othersuch systems may be used and the scope of protection afforded to thepresent inventions is not in anyway limited to, or dependent upon, theuse of QIIME.

Compiling the Sample Metadata Mapping File

The first step in the bioinformatics stage of a microbial communityanalysis study is to consolidate the sample metadata in a spreadsheet.The sample metadata is all per-sample information, including technicalinformation such as the barcode assigned to each sample, and“environmental” metadata. This environmental metadata will differdepending on the types of samples that are being analyzed. If, forexample, the study is of microbial communities in soils, the pH andlatitude where the soil was collected could be environment metadatacategories. Alternatively, if the samples are of the human microbiome,environmental metadata may include subject identifiers and collectiontimes. This spreadsheet will be referred to as the sample metadataand/or mapping file in the following sections. An example samplemetadata mapping file is provided as Table 1.

TABLE 1 Sample Metadata Mapping File #Sample Barcode ID SequenceLinkerPrimerSequence texture depth TOT_ORG_SPECIFIC_LOCATION IT2ACGTGCCGTAGA CATGCTGCCTCCCGTAGGAGT loamy 0-0.05  39.1  Itasca Lake State Park, MN USA (SEQ ID NO: (SEQ ID NO: 11) sand10 HI3 ACGCTATCTGGA CATGCTGCCTCCCGTAGGAGT loamy 0-0.05 182.4  Kohala Peninsula, HI USA (SEQ ID NO: (SEQ ID NO: 13) sand 12 MD2ACTCGATTCGAT CATGCTGCCTCCCGTAGGAGT sandy 0-0.05   4.2  Mojavo Desert, CA USA (SEQ ID NO: (SEQ ID NO: 15) loam 14 CA1ACACGAGCCACA CATGCTGCCTCCCGTAGGAGT silt 0-0.05  16.7  Cedar Mtn, AZ, USA (SEQ ID NO: (SEQ ID NO: 17) loam 16 PE3AGACTGCGTACT CATGCTGCCTCCCGTAGGAGT clay 0-0.05  93.6  Manu National Park, Peru (SEQ ID NO: (SEQ ID NO: 19) loam 18 CO1ACATGATCGTTC CATGCTGCCTCCCGTAGGAGT sand 0-0.05  15.9  Fort Collins, CO USA (SEQ ID NO: (SEQ ID NO: 21) 20 DF3ACCGCAGAGTCA CATGCTGCCTCCCGTAGGAGT loamy 0-0.05  17    Duke Forest, NC USA (SEQ ID NO: (SEQ ID NO: 23) sand 22 PE1ACTTGTAGCAGC CATGCTGCCTCCCGTAGGAGT sandy 0-0.05 134.2  Manu National Park, Peru (SEQ ID NO: (SEQ ID NO: 25) loam 24 SP2AGCGCTGATGTG CATGCTGCCTCCCGTAGGAGT loamy 0-0.05  81    Sequola National Park, CA USA (SEQ ID NO: (SEQ ID NO: 27) sand26 CO3 ACATTCAGCGCA CATGCTGCCTCCCGTAGGAGT sandy 0-0.05   8.2  Shortgrass Steppe LTFR, CO USA (SEQ ID NO: (SEQ ID NO: 29) loam28 SA2 AGATCGGCTCGA CATGCTGCCTCCCGTAGGAGT sand 0-0.05  25    Sunset Crater, AZ USA (SEQ ID NO: (SEQ ID NO: 31) 30 CM1ACATCACTTAGC CATGCTGCCTCCCGTAGGAGT silty 0-0.05  29.9  Clymer Meadow Preserve, TX USA (SEQ ID NO: (SEQ ID NO: 33) clay32 LQ2 ACTCACGGTATG CATGCTGCCTCCCGTAGGAGT silty 0-0.05  41.1  Luquillo LTER, Puerto Rico (SEQ ID NO: (SEQ ID NO: 35) clay 34loam SR2 AGCTATCCACGA CATGCTGCCTCCCGTAGGAGT sandy 0-0.05  14.6  Sedgwig Reserve, CA USA (SEQ ID NO: (SEQ ID NO: 37) loam 36 CH1ACCACATACATC CATGCTGCCTCCCGTAGGAGT loam 0-0.05  28.3  Coffey Ranch, TX USA (SEQ ID NO: (SEQ ID NO: 39) 38 VC1AGGTGTGATCGC CATGCTGCCTCCCGTAGGAGT sandy 0-0.05  56.7  Valles Caldera, NM USA (SEQ ID NO: (SEQ ID NO: 41) loam 40 IE2ACGTCTGTAGCA CATGCTGCCTCCCGTAGGAGT sandy 0-0.05  40.7  Institute for Ecosystem Studies, N (SEQ ID NO: (SEQ ID NO: 43)loam 42 RT2 AGAGTCCTGAGC CATGCTGCCTCCCGTAGGAGT silty 0-0.05  37.5  USDA Grassland Research Center, (SEQ ID NO: (SEQ ID NO: 45) clay44 loam BB1 AAGAGATGTCGA CATGCTGCCTCCCGTAGGAGT sandy 0-0.05  12.84 Bear Brook, ME (SEQ ID NO: (SEQ ID NO: 47) loam 46 CC1ACACTAGATCCG CATGCTGCCTCCCGTAGGAGT sand 0-0.05  19.1  Cedar Creek LTER, MN USA (SEQ ID NO: (SEQ ID NO: 49) 48 TL2AGGACGCACTGT CATGCTGCCTCCCGTAGGAGT silt 0-0.05 158.3  Toollk Lake LTER, AK USA (SEQ ID NO: (SEQ ID NO: 51) loams 50PE6 AGAGAGCAAGTG CATGCTGCCTCCCGTAGGAGT clay 0-0.05  33.4  Manu National Park, Peru (SEQ ID NO: (SEQ ID NO: 53) 52 HI1ACGCGATACTGG CATGCTGCCTCCCGTAGGAGT loam 0-0.05  11.4  Kohala Peninsula, HI USA (SEQ ID NO: (SEQ ID NO: 55) 54 PE7AGAGCAAGAGCA CATGCTGCCTCCCGTAGGAGT silty 0-0.05  63.8  Manu National Park, Peru (SEQ ID NO: (SEQ ID NO: 57) clay 56 BF1AATCAGTCTCGT CATGCTGCCTCCCGTAGGAGT loam 0-0.05  64.4  Bousson Forest, PA, USA (SEQ ID NO: (SEQ ID NO: 59) 58 TL1AGCTTGACAGCT CATGCTGCCTCCCGTAGGAGT loam 0-0.05  70.2  Toollk Lake LTER, AK USA (SEQ ID NO: (SEQ ID NO: 61) 60 KP1ACTACAGCCTAT CATGCTGCCTCCCGTAGGAGT silt 0-0.05  61.2  Konza Prairie LTER, KS USA (SEQ ID NO: (SEQ ID NO: 63) loam 62CL3 ACAGTGCTTCAT CATGCTGCCTCCCGTAGGAGT loamy 0-0.05  12.1  Calhoun Experimental Forest, SC (SEQ ID NO: (SEQ ID NO: 65) sand64

Barcode Decoding and Quality Control

Next, in a combined analysis step, sequence barcodes will be read toidentify the source sample of each sequence, poor quality regions ofsequence reads will be trimmed, and poor quality reads will bediscarded. These steps will be combined for computational efficiency.The features included in quality filtering include whether the barcodewill unambiguously be mapped to a sample barcode, per-base qualityscores, and the number of ambiguous (N) base calls. The default settingsfor all quality control parameters in QIIME will be determined bybenchmarking combinations of these parameters on artificial (i.e.,“mock”) community data, where microbial communities were created in thelab from known concentrations of cultured microbes, and the compositionof the communities is thus known in advance.

Sequence Clustering or “OTU Picking”

After mapping sequence reads to samples and performing quality control,sequences will be clustered into OTUs (Operational Taxonomic Units)based on sequence similarity. This is typically the most computationallyexpensive step in microbiome data analysis, and will be performed toreduce the computational complexity at subsequent steps. The assumptionmade at this stage is that organisms that are closely related, asdetermined by the similarity of their marker gene sequences, arefunctionally similar. Highly similar sequences (e.g., those that aregreater than 97% identical to one another, or other value that isdetermined to be most efficient and meaningful) will be clustered, thecount of sequences that are contained in each cluster will be retained,and then a single representative sequence from that cluster will bechosen for use in downstream analysis steps such as taxonomic assignmentand phylogenetic tree construction. This process of clustering sequencesis referred to as OTU picking, where the OTUs (i.e., the clusters ofsequences) are considered to approximately represent taxonomic unitssuch as species.

There are three high-level strategies for OTU picking, each of which isimplemented in QIIME. In a de novo OTU picking process, reads will beclustered against one another without any external reference sequencecollection. The QIIME workflow pick_de_novo_otus.py is the primaryinterface for de novo OTU picking in QIIME, and includes taxonomyassignment, sequence alignment, and tree-building steps. A benefit of denovo OTU picking is that all reads are clustered. A drawback is thatthere is no existing support for running the clustering in parallel, soit can be too slow to apply to large datasets (e.g., more than 10million reads), although other portions of the workflow areparallelized. De novo OTU picking must be used if there is no referencesequence collection to cluster against, for example because aninfrequently used marker gene is being used. De novo OTU picking cannotbe used if the comparison is between non-overlapping amplicons, such asthe V2 and the V4 regions of the 16S rRNA gene or for very large datasets, like a full HiSeq™ 2000 run. Although technically, de novo OTUpicking can be used for very large data sets, the program would take toolong to run to be practical.

In a closed-reference OTU picking process, reads will be clusteredagainst a reference sequence collection and any reads that do not hit asequence in the reference sequence collection are excluded fromdownstream analyses, pick_closed_reference_otus.py is the primaryinterface for closed-reference OTU picking in QIIME. If the userprovides taxonomic assignments for sequences in the reference database,those are assigned to OTUs. Closed-reference OTU picking must be used ifnon-overlapping amplicons, such as the V2 and the V4 regions of the 16SrRNA, will be compared to each other. The reference sequences must spanboth of the regions being sequenced. Closed-reference OTU picking cannotbe used if there is no reference sequence collection to cluster against,for example because an infrequently used marker gene is being used. Abenefit of closed-reference OTU picking is speed in that the picking isfully parallelizable, and therefore useful for extremely large datasets. Another benefit is that because all OTUs are already defined inthe reference sequence collection, a trusted tree and taxonomy for thoseOTUs may already exist. There is the option of using those, or buildinga tree and taxonomy from the sequence data. A drawback toreference-based OTU picking is that there is an inability to detectnovel diversity with respect to the reference sequence collection.Because reads that do not hit the reference sequence collection arediscarded, the analyses only focus on the diversity that is alreadyknown. Also, depending on how well-characterized the environment is, asmall fraction of the reads (e.g.; discarding 1-10% of the reads iscommon for 16S-based human microbiome studies, where databases likeGreengenes cover most of the organisms that are typically present) or alarge fraction of your reads (e.g., discarding 50-80% of the reads hasbeen observed for “unusual” environments like the Guerrero Negromicrobial mats) may be discarded.

The third method widely used is an open-reference OTU picking process,reads will be clustered against a reference sequence collection and anyreads which do not hit the reference sequence collection aresubsequently clustered de novo. Using appropriate parameters theworkflow pick_de_novo_otus.py (despite the name) is the primaryinterface for open-reference OTU picking in QIIME, and includes taxonomyassignment, sequence alignment, and tree-building steps. Open-referenceOTU picking with pick_de_novo_otus.py is the preferred strategy for OTUpicking. Open-reference OTU picking cannot be used for comparingnon-overlapping amplicons, such as the V2 and the V4 regions of the 16SrRNA, or when there is no reference sequence collection to clusteragainst, for example because an infrequently used marker gene is beingused. A benefit of open-reference OTU picking is that all reads areclustered. Another benefit is speed. Open-reference OTU picking ispartially run in parallel. In particular, if the script is used in asubsampled manner, open reference OTU picking process implemented inpick_de_novo_otus.py is much faster than a the de novo OTU pickingstrategy described above as some strategies are applied to run severalpieces of the workflow in parallel. However, a drawback ofopen-reference OTU picking is also speed. Some steps of this workflowrun serially. For data sets with a lot of novel diversity with respectto the reference sequence collection, this can still take days to run.

Generally, uclust is the preferred method for performing OTU picking.QIIME's uclust-based open reference OTU picking protocol will be usedwhen circumstances allow (i.e., when none of the cases above, where openreference OTU picking is not possible, apply).

The OTU-picking protocol described above is used for processingtaxonomic marker gene sequences such as those from the 16S rRNA, ITS andLSU gene as well as other marker genes amplification sequencing. In thatcase, the sequences themselves are not used to identify biologicalfunctions performed by members of the microbial community; they areinstead used to identify which kinds of organisms are present, as wellas the abundances of those organisms.

In the case of shotgun metagenomic sequencing, the data obtained arerandom fragments of all genomic DNA present in a given microbiome. Thesecan be compared to reference genomes to identify the types of organismspresent in a manner similar to marker gene sequences, but they may alsobe used to infer biological functions encoded by the genomes of microbesin the community. Typically this is done by comparing them to referencegenomes and/or individual genes or genetic fragments that have beenannotated for functional content. In the case of shotgunmetatranscriptomic sequencing, the data obtained are similar to that forshotgun metatranscriptomic sequencing except that the RNA rather thanthe DNA is used, and physical or chemical steps to deplete particularclasses of sequence such as eukaryotic messenger RNA or ribosomal RNAare often used prior to library construction for sequencing. In the caseof shotgun metaproteomics, protein fragments are obtained and matched toreference databases. In the case of shotgun metabolomics, metabolitesare obtained by biophysical methods including nuclear magnetic resonanceor mass spectrometry. In all of these cases, some type ofcoarse-graining of the original data equivalent to OTU picking toidentify biologically relevant features is employed, and a biologicalobservation matrix as described above relating either the raw orcoarse-grained observations to samples is obtained. The steps downstreamfrom the Biological Observation Matrix, including the construction ofdistance matrices, taxon or functional tables, and industry-specific,actionable models from such data, are conceptually equivalent for eachof these datatypes and are within the scope of the present Invention.

Choosing OTU Representative Sequences, Assigning Taxonomy, AligningSequences, and Constructing Phylogenetic Trees

Next, the centroid sequence in each OTU will be selected as therepresentative sequence for that OTU. The centroid sequence will bechosen so that all sequences are within the similarity threshold totheir representative sequence, and the centroid sequences arespecifically chosen to be the most abundant sequence in each OTU.

The OTU representative sequences will next be aligned using an alignmentalgorithm such as the PyNAST software package. PyNAST is areference-based alignment approach, and is chosen because it achievessimilar quality alignments to non-reference-based alignment approaches(e.g., muscle), where quality is defined as the effect of the alignmentalgorithm choice on the results of phylogenetic diversity analyses, butis easily run in parallel, which is not the case for non-reference-basedalignment algorithms.

Once a PyNAST alignment is obtained, positions that mostly contain gaps,or too high or too low variability, will be stripped to create aposition-filtered alignment. This position-filtered alignment will beused to construct a phylogenetic tree using FastTree. This tree relatesthe OTUs to one another, will be used in phylogenetic diversitycalculations (discussed below), and is referred to below as the OTUphylogenetic tree.

In addition to being aligned, all OTU representative sequences will havetaxonomy assigned to them. This can be performed using a variety oftechniques, though our currently preferred approach is the uclust-basedconsensus taxonomy assigner implemented in QIIME. Here, allrepresentative sequences (the “query” sequences) are queried against areference database (e.g., Greengenes, which contains near-full length16S rRNA gene sequences with human-curated taxonomic assignments; UNITEdatabase for ITS; SILVA for 18S rRNA) with uclust. The taxonomyassignments of the three best database hits for each query sequences arethen compared, and a consensus of those assignments is assigned to thequery sequence.

Constructing a Biological Observation Matrix (BIOM) Table

The last of the “upstream” processing steps is to create a BiologicalObservation Matrix (BIOM) table, which contains counts of OTUs on aper-sample basis and the taxonomic assignment for each OTU. This table,which will be referred to as the BIOM table, the OTU phylogenetic treeconstructed above, and the sample metadata mapping file will be the datarequired for computing phylogenetic diversity metrics in the next steps,and for doing visual and statistical analysis based on these diversitymetrics. Although the BIOM is a specific file format for the table withOTU counts on a per-table basis, other file formats are also possible aswell.

Analysis of Microbial Communities

Once a BIOM table, an OTU phylogenetic tree, and a sample metadatamapping file are compiled, the microbial communities present in eachsample will be analyzed and compared (n-dimensional plot). Theseanalyses include, but are not limited to, summarizing the taxonomiccomposition of the samples, understanding the “richness” and “evenness”of samples (defined below), understanding the relative similaritybetween communities (or samples), and identifying organisms or groups oforganisms that are significantly different across community types. Thedifferent types of analysis on soil microbial community data will beillustrated in Example 17.

Taxonomic Composition of Samples

The taxonomic composition of samples is often something that researchersare most immediately interested in can be studied at various taxonomiclevels (e.g., phylum, class, species) by collapsing OTUs in the BIOMtable based on their taxonomic assignments. The abundance of each taxonon a per-sample basis is then typically presented in bar charts, areacharts or pie charts, though this list is not comprehensive. FIG. 14contains an area chart illustrating the phylum level composition of 88soil samples spanning a pH gradient.

FIG. 14 is an illustration of an embodiment of microbiome composition.The y-axis is relative abundance of specific microbial phyla (ahigh-level taxonomic group; each phylum contains many bacterialspecies); the x-axis represents soil pH; and the colors (grey scale andsimplified for purposes of patent figures) present different bacterialphyla.

For example these phyla include:

k_Bacteria;p_AD3

k_Bacteria;p_Acidobacteria

k_Bacteria;p_Actinobacteria

k_Bacteria;p_Armatimonadetes

k_Bacteria;p_BHI80-139

k_Bacteria;p_BRCI

k_Bacteria;p_Bacteroidetes

k_Bacteria;p_Chlorobi

k_Bacteria;p_Chloroflexi

k_Bacteria;p_Cyanobacteria

k_Bacteria;p_Elusimicrobia

k_Bacteria;p_FBP

k_Bacteria;p_FCPU426

k_Bacteria;p_Fibrobacteres

k_Bacteria;p_Firmicutes

k_Bacteria;p_GAL15

k_Bacteria;p_GN02

k_Bacteria;p_Gemmatimonadetes

k_Bacteria;p_Kazan-3B-28

k_Bacteria;p_MVP-21

k_Bacteria;p_NC10

k_Bacteria;p_NKB19

k_Bacteria;p_Nitrospirae

k_Bacteria;p_ODI

k_Bacteria;p_OPII

k_Bacteria;p._0P3

k_Bacteria;p_0P8

k_Bacteria;p_Planctomycetes

k_Bacteria;p_Proteobacteria

k_Bacteria;p_SRI

k_Bacteria;p_Spirochaetes

k_Bacteria;p_TM6

k_Bacteria;p_TM7

Unassigned;Other

k_Bacteria;Other

k_Bacteria;p_

As seen in FIG. 14, each microbial taxon is denoted by a different color(e.g., area, 1401, 1402, 1403, 1404, 1405 for purposes of patentfigures), with the x-axis representing increasing pH and the y-axisrepresenting relative abundance. Some taxa change in a consistent wayfrom low to high pH, for example, Acidobacteria is represented in area1402. These consistent changes can drive the pattern in PCoA.

Within-Sample Diversity (Richness and Evenness):

Alpha diversity refers to diversity of single samples (i.e.,within-sample diversity), including features such as taxonomic richnessand evenness. There are a number of different ways to measure alphadiversity, including but not limited to: Chao 1, Simpson's DiversityIndex and the Shannon Index. The species richness is a measure of thenumber of different species of microbes in a given sample. Typicallythese measures will be performed after rarefaction, or the randomsubsampling of a specified number of sequences. Species evenness refersto how close the relative abundance of a set of species are in aparticular area or environment.

Measures of alpha diversity (or, a measure of within-sample diversity)have a long history in ecology. Alpha diversity measures have been shownto differ in different types of communities, for example, from differenthuman body habitats. For instance, skin-surface bacterial communitieshave been found to be significantly more rich (i.e., containing morespecies; increased diversity) in females than in males, and at dry sitesrather than sebaceous sites, and the gut microbiome of lean individualshave been found to be significantly more rich than those of obeseindividuals.

FIGS. 10 and 11 illustrate ways of viewing alpha diversity.

In this figures, two indices will be used to compare community-levelbacterial richness across 88 different soils. First the number ofobserved OTUs will be computed, based on OTUs clustered with an openreference OTU picking protocol at the 97% sequence similarity level. Thenumber of observed OTUs are shown in FIG. 10. The legend for FIG. 10 isthe x axis is Soil pH; and the y-axis is Observed OTUs. The x-axisrepresents the number of OTUs observed (a measure of “alpha diversity”);the x-axis represents the pH of a soil sample; and each box 1001, 1002,1003, 1004, 1005, represents the distribution of number of OTUs observedin soils of the corresponding pH. The rectangles extend from the lowerto upper quartile values of the data, with a lines 1001 a, 1002 a, 1003a, 1004 a, 1005 a, 1006 a (pH with no distribution, n=1), at the median.The whiskers (dashed lines, e.g., 1001 c, 1001 d) extend from the box to1.5 times the interquartile range. Outliers (those that are outside of1.5 times the interquartile range) are the pluses, e.g., 1001 b, pastthe end of the whiskers. This plot illustrates that the number of OTUspeaks at neutral pH. This index of diversity is limited in that itcharacterizes diversity at only a single level of taxonomic resolution.Diversity will also be computed using Faith's index of phylogeneticdiversity (Faith's PD), which provides an integrated index of thephylogenetic breadth contained within each community.

An example of the computation of the phylogenetic diversity is shown inFIG. 11. Thus, FIG. 11 is an embodiment of a graph of an embodiment ofthe association of environmental parameters with microbial compositionacross 88 soil samples included in a global survey of soil microbialdiversity. The legend for FIG. 11 is the x-axis is Soil pH; and they-axis is Phylogenetic Diversity. The y-axis represents the phylogeneticdiversity observed (a measure of “alpha diversity”); the x-axisrepresents the pH of a soil sample; and each box 1101, 1102, 1103, 1104,1105, represents the distribution of the observed phylogenetic diversityin soils of the corresponding pH. The rectangles extend from the lowerto upper quartile values of the data, with a lines 1101 a, 1102 a, 1103a, 1104 a, 1105 a, 1106 a (pH with no distribution, n=1), at the median.The whiskers (dashed lines, e.g., 1101 c, 1101 d) extend from the box to1.5 times the interquartile range. Outliers (those that are outside of1.5 times the interquartile range) are the pluses, e.g., 1103 d, pastthe end of the whiskers. As in FIG. 10, this plot illustrates that thephylogenetic diversity peaks at neutral pH.

Here we show that the degree of phylogenetic diversity in a sample (aphylogeny-aware measure of richness) changes with soil pH, for 88 soilsranging from pH around 6.5 through 9.5, with a peak in richness aroundneutral pH of 7. These data suggest that in some cases alpha diversitywill be useful input features for building predictive models viasupervised classifiers.

In both cases, the diversity metrics will be calculated for a randomlyselected subset of the same number of sequences per soil sample, here934, because diversity is unavoidably correlated with the number ofsequences collected. The results of these analyses are presented inFIGS. 10-11, and both richness metrics show similar patterns in thisspecific case. By using a set number of sequences, general diversitypatterns will be compared even if it is highly unlikely that the fullextent of diversity was surveyed in each community.

-   -   Between-sample diversity (UniFrac and Principal Coordinates        Analysis)

Generally the primary question of interest when beginning a survey ofnew microbial community types is what environmental features areassociated with differences in the composition of microbial communities?This is a question of between-sample (or “beta”) diversity. Betadiversity metrics provide a measure of community dissimilarity, allowinginvestigators to determine the relative similarity of microbialcommunities. Metrics of beta diversity are pairwise, operating on twosamples at a time.

The difference in overall community composition between each pair ofsamples can be determined using the phylogenetically-aware UniFracdistance metric, which allows researchers to address many of thesebroader questions about the composition of microbial communities.UniFrac calculates the fraction of branch length unique to a sampleacross a phylogenetic tree constructed from each pair of samples. Inother words, the UniFrac metric measures the distance betweencommunities as the percentage of branch length that leads to descendantsfrom only one of a pair of samples represented in a single phylogenetictree, or the fraction of evolution that is unique to one of themicrobial communities. Phylogenetic techniques for comparing microbialcommunities, such as UniFrac, avoid some of the pitfalls associated withcomparing communities at only a single level of taxonomic resolution andprovide a more robust index of community distances than traditionaltaxon-based methods, such as the Jaccard and Sörenson indices. Unlikephylogenetic techniques, species-based methods that measure the distancebetween communities based solely on the number of shared taxa do notconsider the amount of evolutionary divergence between taxa, which canvary widely in diverse microbial populations. Among the firstapplications of phylogenetic information to comparisons of microbialcommunities were the Phylogenetic (P)—test and the F_(ST) test. Pairwisesignificance tests are limited because they cannot be used to relatemany samples simultaneously. Although phylogenetically-aware techniquessuch as UniFrac offer significant benefits, techniques lackingphylogenetic awareness can also be implemented with success: after analternative distance metric (e.g. Bray-Curtis, Jensen-Shannondivergence) has been applied, the resulting inter-sample distance matrixis processed in the same way as a UniFrac distance matrix as describedbelow.

QIIME implements the UniFrac metric and uses multivariate statisticaltechniques to determine whether groups of microbial communities aresignificantly different. When studying a set of n microbial communities,the UniFrac distances between all pairs of communities are computed toderive a distance matrix (using UniFrac or other distances) for allsamples. This will be an n×n matrix, which is symmetric (because thedistance between sample A and sample B is always equal to the distancebetween sample B and sample A) and will have zeros on the diagonal(because the distance between any sample and itself is always zero). Forany reasonably larger value of n (e.g., n>5) it becomes difficult tointerpret patterns of beta diversity from a distance matrix directly(FIG. 9). FIG. 9 shows matrix formed from unweighted UniFrac distancesbetween the first 12 of the 88 soil samples included in the analysis inExample 9. As the number of samples increases beyond just a few (e.g.,five) samples, it becomes very difficult to identify meaningful patternsfrom distance matrices alone.

Ordination techniques, such as principal coordinates analysis (PCoA) andnon-metric multidimensional scaling (NMDS), together with approximationsto these techniques that reduce computational cost or improveparallelism, will be used to summarize these patterns in two or threedimensional scatter plots. The patterns can also be represented in twodimensions using, for example, using line graph, bar graphs, pie charts,Venn diagrams, etc., as a non-exhaustive list. The patterns can also berepresented in three dimensions using, for example, wire frame, ball andstick models, 3-D monitors, etc. This list is also non-exhaustive anddoes not limit the 2-D or 3-D forms by which the data can berepresented.

PCoA is a multivariate analysis technique for finding the most importantorthogonal axes along which samples vary. Distances are converted intopoints in a space with a number of dimensions one less than the numberof samples. The principal coordinates or axes, in descending order,describe how much of the variation (technically, the inertia) each ofthe axes in this new space explains. The first principal coordinateseparates the data as much as possible; the second principal coordinateprovides the next most separation along an orthogonal axis, and soforth. QIIME returns information on all principal axes in a data table.It also allows easy visualization of that data in interactive scatterplots that allow users to choose which principal components to display.The points (each representing a single sample) are marked with coloredsymbols, (grey scale symbols are used for the purposes of the patentfigures) and users can interactively change the colors of the points todetect associations between sample microbial composition and samplemetadata. PCoA often reveals patterns of similarity that are difficultto see in a distance matrix (see, e.g., FIGS. 12 and 13), and the axesalong which variation occurs can sometimes be correlated withenvironmental variables such as pH or temperature. Industrial variables,or control data, can include presence of oil, pressure, viscosity, etc.These control data can be filtered or removed in order to observe othercontrol data factors to visualize possible patterns.

New ways of exploring and visualizing results and identifying meaningfulpatterns are increasingly important as the size and complexity ofmicrobial datasets rapidly increase. QIIME 1.8.0 (released in December2013) introduces several powerful tools to assist in visualizations ofthe results of PCoA, primarily the Emperor 3D scatter plot viewer(https://github.com/qiime/emperor). This includes (i) the ability tocolor large collections of samples using different user-definedsubcategories (for example, coloring environmental samples according totemperature or pH), (ii) automatic scaled/unscaled views, whichaccentuate dimensions that explain more variance, (iii) the ability tointeractively explore tens of thousands of points (and user-configurablelabels) in 3D, and (iv) parallel coordinates displays that allow thedimensions that separate particular groups of environments to be readilyidentified.

The significance of patterns identified in PCoA can be tested with avariety of methods. The significance of the clusters identified byUniFrac can be established using Monte Carlo based t-tests, wheresamples are grouped into categories based on their metadata, anddistributions of distances within and between categories are compared.For example, if a relationship using PCoA is noted between microbialcommunities in soils from an oil well and soils unassociated with oil,the distribution of UniFrac distances between soils from the same groupcan be compared to those between soils from different groups bycomputing a t-score (the actual t-score). The sample labels (oil and notoil) can then be randomly shuffled 10,000 times, and a t-scorecalculated for each of these randomized data sets (the randomizedt-scores). If the oil soils and non-oil soils are significantlydifferent from one another in composition, the actual t-score shouldhigher than the vast majority of the randomized t-scores. A p-value willbe computed by dividing the number of randomized t-scores that arebetter than the actual t-score by 9999. The Monte Carlo simulationsdescribed here will be run in parallel, and are not limited to pairs ofsample categories, so they support analysis of many different sampletypes.

If the samples fall along a gradient that is correlated with someenvironmental metadata or variable (e.g., pH, salinity, temperature,geochemical measures, etc.), rather than clustering into discrete groups(as described above), there are alternative approaches to testing forstatistical significance. For example, if pH appears to be correlatedwith the principal coordinate 1 (PC1) values in a PCoA plot, anempirical (as is sometimes defined in a broader category known as, MonteCarlo simulation)-based Pearson or Spearman correlation test will beperformed. Here, pH and PC1 will be tested to, for example, compute aSpearman rho value. The labels of the samples will again be shuffled10,000 times and rho computed for each randomized data set. The p-valuefor the pH versus PC1 correlation will then be the number of randomizedrho values that are higher than the actual rho value divided by 9999.

Identifying features that are predictive of environment characteristics(i.e., sample metadata)

Supervised classification is a machine learning approach for developingpredictive models from training data. Each training data point consistsof a set of input features, for example, the relative abundance of taxa,and a qualitative dependent variable giving the correct classificationof that data point. In microbiome analysis, such classifications mightinclude soil nutrients, the presence of oil, predominant weatherpatterns, disease states, therapeutic results, or forensicidentification. The goal of supervised classification is to derive somefunction from the training data that can be used to assign the correctclass or category labels to novel inputs (e.g. new samples), and tolearn which features, for example, taxa, discriminate between classes.Common applications of supervised learning include text classification,microarray analysis, and other bioinformatics analyses. For example,when microbiologists use the Ribosomal Database Project website toclassify 16S rRNA gene sequences taxonomically, a form of supervisedclassification is used.

The primary goal of supervised learning is to build a model from a setof categorized data points that can predict the appropriate categorymembership of unlabeled future data. The category labels can be any typeof important metadata, such as pressure, viscosity, pH or temperature.The ability to classify unlabeled data is useful whenever alternativemethods for obtaining data labels are difficult or expensive.

This goal of building predictive models is very different from thetraditional goal of fitting an explanatory model to one's data set. Theconcern is less with how well the model fits our particular set oftraining data, but rather with how well it will generalize to novelinput data. Hence, there is a problem of model selection. A model thatis too simple or general is undesirable because it will fail to capturesubtle, but important information about the independent variables(underfitting). A model that is too complex or specific is alsoundesirable because it will incorporate idiosyncrasies that are specificonly to the particular training data (overfitting). The expectedprediction error (EPE) of the model on future data must be optimized.

When the labels for the data are easily obtained, a predictive model isunnecessary. In these cases, supervised learning will still be usefulfor building descriptive models of the data, especially in data setswhere the number of independent variables or the complexity of theirinteractions diminishes the usefulness of classical univariatehypothesis testing. Examples of this type of model can be seen in thevarious applications of supervised classification to microarray data, inwhich the goal is to identify a small, but highly predictive subset ofthe thousands of genes profiled in an experiment for furtherinvestigation. In microbial ecology, the analogous goal is to identify asubset of predictive taxa. In these descriptive models, accurateestimation of the EPE is still important to ensure that the associationof the selected taxa with the class labels is not just happenstance orspurious. This process of finding small but predictive subsets offeatures, called feature selection, is increasingly important as thesize and dimensionality of microbial community analyses continue togrow.

A common way to estimate the EPE of a particular model is to fit themodel to a subset (e.g., 90%) of the data and then test its predictiveaccuracy on the other 10% of the data. This can provide an idea of howwell the model would perform on future data sets if the goal is to fitit to the entire current data set. To improve the estimate of the EPE,this process will be repeated a number of times so that each data pointis part of the held-out validation data once. This procedure, known ascross-validation, will allow for the comparison of models that use verydifferent inner machinery or different subsets of input features. Ofcourse if many different models are tried and one provides the lowestcross-validation error for the entire data set is selected, it is likelythat the reported EPE will be too optimistic. This is similar to theproblem of making multiple comparisons in statistical inference; somemodels are bound to fortuitously match a particular data set. Hence,whenever possible, an entirely separate test set will be held out forestimating the EPE of the final model, after performing model selection.

Even if the method for selecting the best parameters or degree ofcomplexity for a particular kind of model is determined, there is stilla general challenge of picking what general class of models is mostappropriate for a particular data set. The core aspect of choosing theright models for microbiome classification is to combine the knowledgeof the most relevant constraints (e.g., data sparseness) inherent in thedata with the understanding of the strengths and weaknesses of variousapproaches to supervised classification. If it is understood whatstructures will be inherent in the data, then models that take advantageof those structures will be chosen. For example, in the classificationof microbiomes, methods that can model nonlinear effects and complexinteractions between organisms will be desired. In another example, thehighly diverse nature of many microbial communities on the human body,models designed specifically to perform aggressive feature selectionwhen faced with high-dimensional data will be most appropriate.Specialized generative models will be designed to incorporate priorknowledge about the data as well as the level of certainty about thatprior knowledge. Instead of learning to predict class labels based oninput features, a generative model will learn to predict the inputfeatures themselves. In other words, a generative model will learn whatthe data “looks like,” regardless of the class labels. One potentialbenefit of generative models such as topic models and deep-layeredbelief nets, will be that they can extract useful information even whenthe data are unlabeled. The ability to use data from related experimentsto help build classifiers for one's own labeled data will be importantas the number of publicly available microbial community data setscontinues to grow.

Machine learning classification techniques will be applied to many typesof microbial community data, for example, to the analysis of soil andsediment samples. For the soil and sediment samples, the samples will beclassified according to environment type using support vector machines(SVMs) and k-nearest neighbors (KNN). Supervised learning will been usedextensively in other classification domains with high-dimensional data,such as macroscopic ecology, microarray analysis, and textclassification.

The goal of feature selection will be to find the combination of themodel parameters and the feature subset that provides the lowestexpected error on novel input data. Feature selection will be of utmostimportance in the realm of microbiome classification due to thegenerally large number of features (i.e., constituent species-leveltaxa, or genes, or transcripts, or metabolites, or some combination ofthese): in addition to improving predictive accuracy, reducing thenumber of features leads to the production of more interpretable models.Approaches to feature selection are typically divided into threecategories: filter methods, wrapper methods, and embedded methods.

As the simplest form of feature selection, filter methods are completelyagnostic to the choice of learning algorithm being used; that is, theytreat the classifier as a black box. Filter methods use a two-stepprocess. First a univariate test (e.g. t-test) or multivariate test(e.g., a linear classifier built with each unique pair of features) willbe performed to estimate the relevance of each feature, and (1) allfeatures whose scores exceed a predetermined threshold will be selectedor (2) the best n features for inclusion in the model will be selected;then a classifier on the reduced feature set will be run. The choice ofn can be determined using a validation data set or cross-validation onthe training set.

Filter methods have several benefits, including their low computationalcomplexity, their ease of implementation, and their potential, in thecase of multivariate filters, to identify important interactions betweenfeatures. The fact that the filter has no knowledge about the classifieris advantageous in that it provides modularity, but it can also bedisadvantageous, as there is no guarantee that the filter and theclassifier will have the same optimal feature subsets. For example, alinear filter (e.g., correlation-based) is unlikely to choose an optimalfeature subset for a nonlinear classifier such as an SVM or a randomforest (RF).

The purpose of a filter will be to identify features that are generallypredictive of the response variable, or to remove features that arenoisy or uninformative. Common filters include, but are not limited to,the between-class χ2 test, information gain (decrease in entropy whenthe feature is removed), various standard classification performancemeasures such as precision; recall, and the F-measure, and the accuracyof a univariate classifier, and the bi-normal separation (BNS), whichtreats the univariate true positive rate and the false-positive rate(tpr, fpr, based on document presence/absence in text classification) asthough they were cumulative probabilities from the standard normalcumulative distribution function, and the difference between theirrespective z-scores. F⁻¹ (tpr)-F⁻¹ (fpr), will be used as a measure ofthat variable's relevance to the classification task.

Wrapper methods are usually the most computationally intensive andperhaps the least elegant of the feature selection methods. A wrappermethod, like a filter method, will treat the classifier as a black box,but instead of using a simple univariate or multivariate test todetermine which features are important, a wrapper will use theclassifier itself to evaluate subsets of features. This leads to acomputationally intensive search: an ideal wrapper will retrain theclassifier for all feature subsets, and will choose the one with thelowest validation error. Were this search tractable, wrappers would besuperior to filters because they would be able to find the optimalcombination of features and classifier parameters. The search will notbe tractable for high-dimensional data sets; hence, the wrapper will useheuristics during the search to find the optimal feature subset. The useof a heuristic will limit the wrapper's ability to interact with theclassifier for two reasons: the inherent lack of optimality of thesearch heuristic, and the compounded lack of optimality in cases wherethe wrapper's optimal feature set differs from that of the classifier.In many cases the main benefit of using wrappers instead of filters,namely that the wrapper can interact with the underlying classifier, isshared by embedded methods, and the additional computational costincurred by wrappers therefore makes such methods unattractive.

Embedded approaches to feature selection will perform an integratedsearch over the joint space of model parameters and feature subsets sothat feature selection becomes an integral part of the learning process.Embedded feature selection will have the advantage over filters that ithas the opportunity to search for the globally optimal parameter-featurecombination. This is because feature selection will be performed withknowledge of the parameter selection process, whereas filter and wrappermethods treat the classifier as a “black box.” As discussed above,performing the search over the whole joint parameter-feature space isgenerally intractable, but embedded methods will use knowledge of theclassifier structure to inform the search process, while in the othermethods the classifier must be built from scratch for every feature set.

Exploration and Production of Hydrocarbons

Microbial communities as physiochemical sensors that can measureimportant production parameters that inform, and can direct at least inpart, decision making during hydrocarbon exploration and production in amanner that can have one or more of the following improvements relativeto existing approaches: (a) be non-invasive or non-disruptive toproduction operations, (b) capture subsurface information at a distanceaway from the well bore, (c) be measured in the production environmentwithout requiring well bore workover, (d) be more cost effective thanexisting measurement approaches, (e) provide more accurate informationabout downhole conditions (g) capture subsurface information at the wellbore and (f) any combination or variation of the above. The followingexamples illustrate some potential embodiments of microbial communitiesas physiochemical sensors.

Example 10

Identifying producing hydrocarbon wells for stimulation andre-stimulation using techniques including hydraulic fracturing is acritical decision facing operators. Currently, many technical variablesare used to determine this decision such as: Young's Modulus, Vitrinitereflectance, total organic content, original hydrocarbon in place, netthickness, average depth, and areal extent. All of the aforementionedvariables can be gathered using current techniques and could beconsidered as operational information or industrial setting information.Young's modulus determines the stress and strain factors of thesubsurface and can be used to determine rock brittleness and theeffectiveness of the formation to fracture under hydraulic load.Vitrinite reflectance is measured to assess the thermal maturity of thereservoir. Total organic content measures the potential organic materialin the subsurface. Original hydrocarbon in place is used to determinethe overall potential of hydrocarbon beneath the subsurface. Netthickness determines the thickness of the formation, which containhydrocarbon. Average depth provides details in the z-axis of a map andareal extent provides details in the x-y dimensions of a map thatindicate the location of hydrocarbon.

Similarly to Example 16 and 17 samples extracted from the well cuttings,drilling mud, circulating mud, core samples, flowback, or producedfluids (including but not limited to, hydrocarbons) during the drillingor production of a subsurface reservoir, will be collected and analyzed.With these samples, key microbial features will be determined for eachwell and, utilizing prior database information and modeling, used tocreate predictive data for candidates for well stimulation andre-stimulation. This predictive or derived data will be used inconjunction with real time and historical data to develop analysis thatdrives production methods and decisions.

Example 11

Conducting the economic evaluation of new or existing oil leases is acritical component of hydrocarbon production. Currently, many technicalvariables are used to determine this decision such as: Young's Modulus,Vitrinite reflectance, total organic content, original hydrocarbon inplace, net thickness, average depth, and areal extent. All of theaforementioned variables can be gathered using current techniques andcould be considered historical or real time operational or industrialsetting information or data. Young's modulus determines the stress andstrain factors of the subsurface and can be used to determine rockbrittleness and the effectiveness of the formation to fracture underhydraulic load. Vitrinite reflectance is measured to assess the thermalmaturity of the reservoir. Total organic content measures the potentialorganic material in the subsurface. Original hydrocarbon in place isused to determine the overall potential of hydrocarbon beneath thesubsurface. Net thickness determines the thickness of the formationwhich contain hydrocarbon. Average depth provides details in the z-axisof a map and areal extent provides details in the x-y dimensions of amap that indicate the location of hydrocarbon.

Similarly to Example 16 and Example 17, samples extracted from wellcuttings, drilling mod, circulating mud, core samples, flowback, orproduced fluids (including but not limited to, hydrocarbons) during thedrilling or production of a subsurface reservoir will be collected andanalyzed. With these samples, key microbial features will be determinedfor each well and, utilizing prior database information and modeling,used to assess the economic viability and potential of new or existingproperties and leases for hydrocarbon production. This predictive orderived data will be used in conjunction with real time and historicaldata to develop analysis that drive exploration and production methodsand decisions.

Example 12

Subsurface flow communication and reservoir connectivity are typicallyparameters that can be important or beneficial to understand whendetermining the value and method of production of a well in a shaleformation. Subsurface flow is the flow of oil beneath the earth'ssurface. Connectivity represents one of the fundamental properties of areservoir that directly affects recovery. If a portion of the reservoiris not connected to a well, it cannot be drained. Connectivityparameters may be defined as the percentage of the reservoir that isconnected, and reservoir connectivity is defined as the percentage ofthe reservoir that is connected to wells and/or fractures stimulatedwithin a well. Currently, many technical variables are used to make thisassessment such as: Geochemical analysis, tracer analysis, andmicroseismic analysis. All of the aforementioned variables can begathered using current techniques and could be considered historical orreal time data. Geochemical analysis is the chemical analysis of thecarbon, salt or other chemical constituents of the hydrocarbon, water,or gas content in the subsurface and used to identify the uniquecharacteristics of the fluids in question. Tracer analysis is the use ofproprietary chemicals, radioactive or otherwise, that are injected intothe subsurface and used to measure flow or other dynamic properties inthe subsurface. Microseismic analysis is the use of seismic data tocharacterize the geophysical and seismic properties of the rockformation during drilling, hydraulic fracturing, or production.

Similarly to Example 16 and Example 17, samples extracted from wellcuttings, circulating mud, core samples; flowback, or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir can be collected and analyzed. Withthese samples, key microbial features will be determined for each welland, utilizing prior database information and modeling, used to createpredictive data for the well's subsurface flow communication andreservoir connectivity. This predictive or derived data will be used inconjunction with real time and historical data to develop analysis thatdrives production methods and decisions.

Example 13

Determining the optimal locations for drilling new wells on existingleases is a critical decision facing operators. This decision is knownby many industrial terms such as downspacing strategy, infill drilling,or infield drilling. All these terms refer to the same general need, tomaximize the effectiveness of future drilling on an existing lease.Currently, many technical variables are used to make this assessmentsuch as: reservoir connectivity, geochemical analysis, tracer analysis,and microseismic analysis. All of the aforementioned variables can begathered using current techniques and could be considered historical orreal time operational or industrial setting information or data.Geochemical analysis is the chemical analysis of the carbon, salt orother chemical constituents of the hydrocarbon, water, or gas content inthe subsurface and used to identify the unique characteristics of thefluids in question. Tracer analysis is the use of proprietary chemicals,radioactive or otherwise, that are injected into the subsurface and usedto measure flow or other dynamic properties in the subsurface.Microseismic analysis is the use of seismic data to characterize thegeophysical and seismic properties of the rock formation duringdrilling, hydraulic fracturing, or production. Connectivity parametersmay be defined as the percentage of the reservoir that is connected, andreservoir connectivity is defined as the percentage of the reservoirthat is connected to wells and/or fractures stimulated within a well

Similarly to Example 16 and Example 17, samples extracted from wellcuttings, circulating mud, core samples, flowback, or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir will be collected and analyzed.With these samples, key microbial features will be determined for eachwell and, utilizing prior database information and modeling, used tocreate predictive data to develop an optimal drilling plan for futurewells on an existing lease. This predictive or derived data will be usedin conjunction with real time and historical data to develop analysisthat drives production methods and decisions.

Example 14

Determining the percent of oil contributed from each zone or compartmentin a formation is a critical analysis method for operators.Understanding of these contribution profiles drives decisions on how tomaximize production from each zone and the ultimate economic potentialof the well. This analysis is particularly challenging in co-mingledproduction streams. Co-mingled production streams refer to theproduction of hydrocarbon from multiple locations, zones, intervals inthe vertical or horizontal dimension of the subsurface. Currently, manytechnical variables are used to assess oil contribution for each zonesuch as: geochemical analysis, and tracer analysis. All of theaforementioned variables can be gathered using current techniques andcould be considered historical or real time data. Geochemical analysisis the chemical analysis of the carbon, salt or other chemicalconstituents of the hydrocarbon, water, or gas content in the subsurfaceand used to identify the unique characteristics of the fluids inquestion. Tracer analysis is the use of proprietary chemicals,radioactive or otherwise, that are injected into the subsurface and usedto measure flow or other dynamic properties in the subsurface.

Similarly to Example 16 and Example 17, samples extracted from wellcuttings, circulating mud, core samples, flowback, or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir will be collected and analyzed.With these samples, key microbial features will be determined for eachwell and, utilizing prior database information and modeling, used tocreate predictive data to assess the percentage of contribution fromeach interval, location, or zone of the subsurface. This predictive orderived data will be used in conjunction with real time and historicaldata to develop analysis that drives production methods and decisions.

Example 15

Determining the optimal locations to hydraulically fracture a newlydrilled well is a critical economic decision of operators. Each stage ofa fracture is economically costly and carry environmental risks sooperators want to identify those stages which are most effective tostimulate. Currently, many techniques are used to assess thecharacteristics of the well bore such as: wireline well logs and loggingwhile drilling (LWD). All of the aforementioned techniques can begathered using current techniques and could be considered historical orreal time data. Wireline well logs refers to the use of measurementdevices along the wellbore that characterize the physical and chemicalproperties of the wellbore, rock formation, and potential forhydrocarbon production. LWD refers to the use of measurement devicesduring the drilling process that characterize the physical and chemicalproperties of the wellbore, rock formation, and potential forhydrocarbon production.

Similarly to Example 16 and Example 17, samples extracted from wellcuttings, circulating mud, core samples, flowback, or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir will be collected and analyzed.With these samples, key microbial features will be determined for eachwellbore and, utilizing prior database information and modeling, used todetermine the optimal locations for hydraulic fracturing. Thispredictive or derived data will be used in conjunction with real timeand historical data to develop analysis that drives production methodsand decisions.

Example 16

In this example, two indices will be used to compare community-levelbacterial richness across 95 different oil samples. First the number ofobserved OTUs will be computed, based on OTUs clustered with an openreference OTU picking protocol at the 97% sequence similarity level.This index of diversity is limited in that it characterizes diversity atonly a single level of taxonomic resolution. Diversity will also becomputed using an index such as Faith's index of phylogenetic diversity(Faith's PD), which provides an integrated index of the phylogeneticbreadth contained within each community.

In both cases, the diversity metrics will be calculated for a randomlyselected subset of the same number of sequences (which is could be basedon rarefaction curves generated from the samples) per oil sample, 1000sequences per sample, for instance, because species richness isunavoidably correlated with the number of sequences collected. By usinga set number of sequences, general diversity patterns will be comparedeven if it is highly unlikely that the full extent of diversity wassurveyed in each community.

Different metadata factors (hydrocarbon concentration and formationdepth, for example) and their effects on microbial community compositionwill be determined using the UniFrac results. As previously discussed,UniFrac quantifies the fraction of unique branch lengths against thetotal branch length between pairs of communities from one phylogenetictree, giving an estimate of the phylogenetic distance between thosecommunities. Separate neighbor-joining phylogenetic trees containing allof the bacterial will be generated with FastTree. Phylogenetic distancesbetween the bacterial communities for each plot will be generated usingweighted and unweighted UniFrac. Dendograms are among the availablemethods of viewing a tree.

If the composition of bacterial communities in this example were highlyvariable across formation depth, they may share only a small percentageof phylotypes (ie 0.9% at the 97% similarity level), although thisdegree of community overlap is likely to be an underestimate given thatnot all phylotypes present in a given sample were identified.Visualization of the pairwise UniFrac distances on PCoA plots wouldindicate significant variability within and across the depth of theformation. Samples from the deepest formations, for example, may harborsimilar microbial communities. However, microbial communities from moreshallow formations yet at similar depths may not necessarily harborsimilar bacterial communities, as the variability between depths couldexceeded the variability within a given range of depth. This patternwould be confirmed by a nonsignificant ANOSIM P value (P>0.05) for deptheffects on UniFrac distances. If the hydrocarbon concentration were moststrongly correlated with the overall UniFrac distances between samples,the PCoA plots would show minimal overlap among communities that differby more than few percent in hydrocarbon concentration when samples arecolored by hydrocarbon content. This effect would be clearly visible ona PCoA plot where the points are colored by hydrocarbon concentration.These plots are easily generated using EMPeror, an open source softwarepackage developed for the visualization of PCoA plots in the context ofsample metadata, or another software which supports exploratory dataanalysis such as this.

FIG. 12 is an embodiment of a Principal Coordinates (PCoA) plot. Eachpoint, e.g., 1201, in this PCoA plot represented one of 88 soil samplesincluded in a global survey of soil microbial diversity. Points that arecloser in space are more similar in phylogenetic composition. Points areshown in varying color (grey scale for purposes of patent figure) basedupon sample pH. It is clear that samples which are more similar inmicrobial composition (i.e., closer in space in the PCoA plot) aresimilar in pH. This illustrates one strategy that can be employed toassociate overall phylogenetic composition with environmentalinformation to identify parameters associated with, driving, or drivenby microbial composition. This plot was generated using Emperor, an opensource software package developed for the visualization of PCoA plots inthe context of sample metadata, which supports exploratory data analysissuch as this.

FIG. 13 is an embodiment of a PCoA plot. Each point, e.g., 1301 in thisPCoA plot represented one of 88 soil samples included in a global surveyof soil microbial diversity. Points that are closer in space are moresimilar in phylogenetic composition. This is the same plot presented inFIG. 10 except that points are now colored (grey scale for purposes ofpatent figure) by the latitude at which the sample was collected, ratherthan pH. It is clear that samples which are more similar in microbialcomposition (i.e., closer in space in the PCoA plot) are not necessarilysimilar in latitude. When compared to FIG. 10, it is clear that pH isfar more strongly associated with microbial composition than islatitude.

Custom analyses with UniFrac will be done as well. The UniFrac anddiversity metrics will be applied to specific lineages of bacteria(Actinobacteria, Alphaproteobacteria, Gamma proteobacteria, andFirmicutes, for example). These lineage-specific analyses will bedistinct from those described previously in that the diversity andphylogenetic composition of these individual taxa across the collectedoil samples will be compared, not just the overall patterns evident fromexamining all taxa together. The taxa selected should be the mostabundant groups of bacteria in the total sequence dataset, oftenreferred to as phyla, recognizing that the term “phyla” is being used ina general manner.

For the lineage-specific UniFrac analyses, the number of sequences willbe determined by randomly selecting sequences per sample depending onthe abundance of a given phyla in a given sample. Normalizing the numberof sequences per sample allows for control for the effects of surveyeffort (number of sequences per phylum per sample) in comparing thelineage-specific UniFrac distances across the sample set. Because somesamples will not have the required number of sequences per phylum, theselineage-specific analyses will be conducted on only a subset of thetotal samples, excluding those samples where the individual phyla wererelatively rare. From the lineage analysis, some taxa may change in aconsistent way from low to high hydrocarbon content, and theseconsistent changes can drive the patterns observed in PCoA plots.

The phylogenetic approaches of UniFrac distances and Faith's PD are morepowerful than standard OTU-based approaches where community structureand diversity are compared at a single level of sequence similaritybecause they take into account different levels of similarity betweendifferent pairs of taxa. In particular, comparing communities bygrouping sequences into OTUs defined at the 97% similarity level haslimitations in that such surveys will be far from comprehensive, andoverarching patterns evident by comparing overall phylogenetic structuremay be more difficult to discern and quantify.

Example 17

In the oil well setting, detailed metadata for each sample will becollected and compiled in a spreadsheet, database, or other system fororganizing tabular or otherwise structured information. Text mining orother techniques may also be used to convert unstructured informationinto structured information for analysis, or the unstructured data maybe analyzed directly. This metadata includes information about samplecollection, the well and formation, chemical and physicalcharacteristics of the fluid, and well productivity. Other associatedmetadata can be gathered from well logs, production, seismic, cores,etc. For each sample, general metadata requirements will include, but isnot limited to: source well identifier; source formation identifier(s);collection source (wellhead or tank); collection date and time;collector name or identifier (to test for collector-specific patterns,which may indicate contamination); and method of collection (if morethan one is used). For each well, general metadata requirements willinclude, but are not limited to: well history; previous experiments atthat particular well; previous well identifiers that were affected bycertain experiments; maps; time in operation; physical characteristicsof fluid, including pressure, temperature, and/or viscosity of thereservoir away from the wellbore and injection locations; chemicalcharacteristics of fluid, including the concentrations and distributionsof specific hydrocarbons, and other parameters previously collected;geological characteristics, including permeability, porosity, locationof oil/water interface; production data, including volume of differenthydrocarbons over time, rate of decline, different recovery operations(primary, secondary, tertiary recovery, etc.); indication of “strange”wells, or those that had surprising or unpredictable performance (forexample, which wells stopped producing rapidly, did not meetproductivity expectations, had unusual chemistries, physics, oil/waterchanges, etc.). Determining the microbial communities will be helpfulfor an assortment of goals, for example, if the microbial profile variesas a function of pressure, temperature, and/or viscosity then it can bean indicator for reservoir rock/fluid conditions. Knowledge of theseparameters can change the flow rates and pressure used in a floodingoperation.

Example 18

An embodiment of an on-site sequencing has a specialized set ofequipment and reagents including but not limited to: sample collectioncontainers, personal protective equipment, pipettors, plasticconsumables (eg pipet tips, conical centrifuge tubes of variousvolumes), electrophoresis equipment, fluorometric measuring devices(single tube and plate readers), centrifuges, PCR hoods, thermocylers,ice machine or peltier cooling unit and water bath or peltier heatingunit for 96 well plates, DNA/RNA extraction reagents, quantificationreagents for genetic material, liquid-handling robot, sequencer(Illumina MiSeq, for instance), compute resources, high speed datatransmission capabilities (land line or satellite based). These itemscould be housed in a 1) a mobile vehicle capable of accessing any siteon which oil and gas exploration or production is being carried out or2) a standard 20 ft intermodal shipping container that can be placedon-site and leveled or 3) a trailer that can be towed onto a worksiteand leveled. In any instance the mobile unit should be modified tosupport sample collection, DNA extraction, PCR and quantification of PCRproduct, and sequencing in an environment suitable for work inmicrobiology or molecular biology. Modifications of primary concern areconsistent electrical supply to run the equipment; use of non-porousmaterial and/or standard laboratory bench material for floors, sides andceilings that can be cleaned and decontaminated with for example DNAseAWAY or bleach solution; have positive pressure with HEPA filtered airflow to minimize the chance of dust and or contaminants and volatilesentering the lab work area and/or a cabinet with such filtering; ananteroom where trained personnel can removed soiled garments and changeinto appropriate laboratory clothing.

Example 19

The microbiome of an oil patch is distinctive and that microbiome can beanalyzed to predict where other oil patches may exist. To develop usefulmicrobial sensors based on oil extracted from wells, essential baselineinformation about compositional differences of fluids across space andtime must be collected. This is necessary to inform future studies ofmicrobial communities at this site. For example, the studies willprovide information about the intra-well temporal dynamics of microbialcommunities, and how those compositional differences relate to theinter-well and inter-formation differences and the associatedcharacteristics, including productivity, of each well. The productionzone that oil was extracted from when it reaches a wellbore will includeproduction-zone-specific microbial indicators that, from an oil sample,could be used to indicate the source production zone. Microbialindicators of pressure, temperature, and/or viscosity that, from an oilsample, will be used to determine the pressure, temperature, and/orviscosity of the reservoir away from the wellbore and injectionlocations.

The predictive power of the microbiome analysis will be used to predictdiscrete variables and continuous variables. In another example, themicrobiome indicators will provide information on primary production,when the location of the water/oil interface changes, so that theconcentration of oil in the extract decreases. Microbial indicators ofthe location of or distance from the oil/water interface will indicatethat the interface has shifted, or that the well is tapped. In anotherexample, microbiome exploratory analysis will be used to determine whatfluid/well parameters or production characteristics may be correlatedwith our microbial indicators. The low specificity, high sensitivitysweep for microbial indicators that are economically useful will providepreliminary data that can be used to perform more robust investigationin future sampling events.

Microbial Measurements as Physiochemical Sensors in a HydrocarbonProduction Setting

Microbial communities as physiochemical sensors that can measureimportant production parameters that inform, and can direct at least inpart, decision making during hydrocarbon exploration and production in amanner that can have one or more of the following improvements relativeto existing approaches: (a) be non-invasive or non-disruptive toproduction operations, (b) capture subsurface information at a distanceaway from the well bore, (c) be measured in the production environmentwithout requiring well bore workover, (d) be more cost effective thanexisting measurement approaches, or (e) provide more accurateinformation about downhole conditions and (f) any combination orvariation of the above. The following examples illustrate some potentialuses of microbial communities as physiochemical sensors.

Example 20

Oil saturation and permeability are typically useful parameters todetermine both well zones that could be attractive candidates forhydraulic fracturing and the potentially more effective methods forhydraulic fracturing. These parameters are also applicable in oilproduction techniques, such as waterflood operations, that do notinvolve or require hydraulic fracturing but require detailed knowledgeof the subsurface to inform production decisions (e.g. off shore oilproduction or on shore production). Oil saturation is the fraction ofthe pore space occupied by oil. Most oil reservoirs also contain someconnate water (non-movable). The oil saturation directly affects thecalculation of reserves. Oil permeability is the property of rocks thatis an indication of the ability for oil to flow through rocks. Highpermeability will allow oil and gases to move rapidly through the rocks.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples, flowback, and/or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir, will be collected and analyzed.With these samples, key microbial features will be determined for eachwell zone and, utilizing prior database information and modeling, usedto create predictive data for oil saturation and permeability. Thispredictive or derived data will be used to drive production methods anddecisions.

Example 21

A reservoirs' wettability is typically a useful parameter in determiningthe permeability, production potential, and most effective method ofhydraulically fracturing a well. Wettability is the preference of asolid to contact one liquid or gas, known as the wetting phase, ratherthan another. The wetting phase will tend to spread on the solid surfaceand a porous solid will tend to imbibe the wetting phase, in both casesdisplacing the nonwetting phase. Rocks can be water-wet, oil-wet orintermediate-wet. The intermediate state between water-wet and oil-wetcan be caused by a mixed-wet system, in which some surfaces or grainsare water-wet and others are oil-wet, or a neutral-wet system, in whichthe surfaces are not strongly wet by either water or oil. Wettabilityaffects relative permeability, electrical properties, nuclear magneticresonance relaxation times and saturation profiles in the reservoir. Thewetting state impacts waterflooding and aquifer encroachment into areservoir. Surfactants or other additives in drilling fluids, especiallyoil-base mud, or other injected fluids can change formation wettability.Wettability change is normally treated with mutual solvents to removethe rock-oil coating (asphaltene or paraffin precipitation), followed bya strong water-wet surfactant to reduce the tendency of furtherhydrocarbon precipitation.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples, flowback, and/or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir will be collected and analyzed.With these samples, key microbial features will be determined for asubsurface reservoir and, utilizing prior database information andmodeling, used to create predictive data for the well's wettability.This predictive or derived data will be used to drive production methodsand decisions.

Example 22

Oil viscosity, temperature, pressure, porosity, oil or water saturation,and compressibility are typically useful parameters for determining thevalue and method of production of a well. Oil viscosity is a frictionalmeasurement of oil flow at a given temperature and determines itsresistance to flow. Water content is expressed as a ratio, which canrange from 0 (completely dry) to the value of the materials' porosity atsaturation. Porosity, or void fraction, is a measure of the void (i.e.,“empty”) spaces in a material, and is a fraction of the volume of voidsover the total volume, between 0 and 1, or as a percentage between 0 and100%. The oil or water content at saturation is the maximum content ableto be held in the subsurface at equilibrium conditions. Compressibilityis the relative change in fluid volume related to a unit change inpressure. This is usually expressed as volume change per unit volume offluid per psi of pressure change. Gas has higher compressibility thanliquid (oil or water).

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples, flowback, and/or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir will be collected and analyzed.With these samples, key microbial features will be determined for eachwell zone and, utilizing prior database information and modeling, usedto create predictive data for the well's oil viscosity, temperature,pressure, porosity, oil or water saturation, and compressibility. Thispredictive or derived data will be used to drive production methods anddecisions.

Example 23

Subsurface flow communication and reservoir connectivity are typicallyparameters that can be important or beneficial to understand whendetermining the value and method of production of a well. Subsurfaceflow is the flow of oil beneath the earth's surface. Connectivityrepresents one of the fundamental properties of a reservoir thatdirectly affects recovery. If a portion of the reservoir is notconnected to a well, it cannot be drained. Connectivity parameters maybe defined as the percentage of the reservoir that is connected, andreservoir connectivity is defined as the percentage of the reservoirthat is connected to wells.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples flowback, and/or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir be collected and analyzed. Withthese samples, key microbial features will be determined for each wellzone and, utilizing prior database information and modeling, used tocreate predictive data for the well's subsurface flow communication andreservoir connectivity. This predictive or derived data will be used todrive production methods and decisions.

Microbial Measurements as Tracers in an Oil and Gas Field

Microbial communities acting as tracers in the oil & gas fields can haveone or more of the following improvements relative to existingapproaches: (a) be environmentally benign, (b) be custom and specific tothe oil reservoir, (c) be more cost effective, (d) provide greaterresolution, and (e) any combination or variation of the above.

Example 24

A well's propensity for producing oil versus gas typically can be acentral parameter when determining the value and method of production ofa well. Both the type of hydrocarbon and total productivity can becritical determinants in a well's potential and the timing to producefrom the well given economic and technical conditions.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples, flowback, and/or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir will be collected and analyzed.With these samples, key microbial features will be determined for eachwell zone and, utilizing prior database information and modeling, usedto create predictive data for the well's propensity for producing oilversus gas. This predictive or derived data will be used to driveproduction methods and decisions.

Example 25

The bacteria that are present in a well can be a key factor whendetermining the value and method of production of a well. Bacteria canhave negative influence on the production of oil and gas. To mitigatetheir effects, biocides can be included in hydraulic fracturingsolutions. Biocides are commonly used in water muds containing naturalstarches and gums that are especially vulnerable to bacterial attack.Biocide choices are limited, and care must be taken to find those thatare effective yet approved by governments and by company policy.Biocides can be used to control sulfate-reducing bacteria, slime-formingbacteria, iron-oxidizing bacteria and bacteria that attacks polymers infracture and secondary recovery fluids. In polymers, the degradation ofthe fluid is controlled, thus avoiding the formation of a large biomass,which could plug the formation and reduce permeability.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples flowback, and/or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir will be collected and analyzed.With these samples, key microbial features will be determined for eachwell zone and, utilizing prior database information and modeling, usedto create predictive data for the bacteria present in a well. Thispredictive or derived data will allow for the more selective use ofbiocides, thereby reducing or changing overall biocide usage whileincreasing production potential.

Example 26

The oil reservoir or zone that a specific well has tapped is typicallyuseful information when determining the value and method of productionof a well. Knowledge of which zone is producing and the quantity of oilremaining in the zone inform waterflood operations. The waterfloodoperations seek to improve the conformance of oil production along thevertical well bore (vertical conformance) as well as ensuring consistentproduction across the breadth wells at the surface (aerial conformance).A well zone is a slab of reservoir rock bounded above and below byimpermeable rock. A production zone's size, permeability, saturation,and propensity to produce oil as well as vertical and aerial conformanceare all factors that determine the optimal number of well's that can beused to produce oil from the reservoir and the methods to waterflood orCO2 flood the reservoir to increase production.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples flowback, and/or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of each zone will be collected and analyzed. With thesesamples, key microbial features will be determined for each well zoneand, utilizing prior database information and modeling, used to createpredictive data about the production zone that improves vertical andaerial conformance. This predictive or derived data will be used todrive production methods and decisions.

Example 27

Tracking treatment fluids and produced water is typically usefulinformation in facilitating production decisions, cleanup, andenvironmental remediation operations. Treatment fluid is a fluiddesigned and prepared to resolve a specific wellbore or reservoircondition. Treatment fluids are typically prepared at the well site fora wide range of purposes, such as stimulation, isolation or control ofreservoir gas or water. Every treatment fluid is intended for specificconditions and should be prepared and used as directed to ensurereliable and predictable performance. Produced water is water producedfrom a wellbore that is not a treatment fluid. The characteristics ofproduced water vary and use of the term often implies an inexact orunknown composition. It is generally accepted that water within thepores of shale reservoirs is not produced due to its low relativepermeability and its mobility being lower than that of gas.

Similarly to Example 16 and Example 17, samples extracted from thecirculating fraced water produced water, and/or other fluids duringdrilling or production will be collected and analyzed. With thesesamples, key microbial features will be determined for the subsurfacereservoir and; utilizing prior database information and modeling, usedto create predictive data about the chemical and physical properties ofthe treatment and produced fluids. This predictive or derived data willbe used to drive production decisions, cleanup, and environmentalremediation operations. Likewise, such data could be used to makedecisions about cleanup, and environmental remediation operations

Example 28

Determining pay zones can be a key factor when determining the value andmethod of production of a well. The overall interval in which paysections occur is the gross pay; the smaller portions of the gross paythat meet local criteria for pay (such as minimum porosity, permeabilityand hydrocarbon saturation) are net pay. Understanding the state oflocal criteria can determine if it is economically advantageous tohydraulically re-fracture a site to increase or prolong oil production.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples, flowback, and/or produced fluids(including but not limited to, hydrocarbons) will be collected andanalyzed. With these samples, key microbial features will be determinedthe subsurface reservoir and, utilizing prior database information andmodeling, used to create predictive data about the pay zones that a wellhas tapped. This predictive or derived data will be used to driveproduction methods and decisions.

Example 29

The prevention of water table and groundwater aquifers contamination canbe a central task in reducing the environmental impact of hydraulicfracturing. Monitoring the microbiomes of the water supplies that arelocal to a hydraulic fracturing site allows energy producers to assessif and how their development has altered local environments. Becausemicrobiomes are particularly susceptible to environmental changes theywell suited to act as early indicators of change.

Similarly to Example 16 and Example 17, samples extracted from the localwater supplies and/or fluids contained around and from wells will becollected and analyzed. With these samples, key microbial features willbe determined for the subsurface reservoir and, utilizing prior databaseinformation and modeling, used to create predictive data about theenvironmental impact of the hydraulic fracturing. This predictive orderived data will be used to limit the environmental impact through theoptimization of production methods.

Example 30

A high-resolution subsurface geologic map of a region is typically auseful tool when determining the value and method of production of awell. Geologic maps show the type and spatial distribution of rocks.Rock formations are color-coded and symbols for geological structuresare annotated, so age relationships are evident. Topographic contourscan also appear on geologic maps. Detailed information about the

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples, flowback, and/or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir will be collected and analyzed.With these samples, key microbial features will be determined for eachwell zone and, utilizing prior database information and modeling, usedto create predictive data that can be transformed into a high resolutionsubsurface geologic map of a production zone. This predictive or deriveddata will be used to drive production methods and decisions.

Example 31

The oil-water contact point can be a key factor when determining thevalue and method of production of a well. The oil-water contact is abounding surface in a reservoir above which predominantly oil occurs andbelow which predominantly water occurs. Although oil and water areimmiscible, the contact between oil and water is commonly a transitionzone and there is usually irreducible water adsorbed by the grains inthe rock and immovable oil that cannot be produced. The oil-watercontact is not always a flat horizontal surface, but instead might betilted or irregular.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples flowback, and/or produced fluids(including but not limited to, hydrocarbons) during the drilling of asubsurface reservoir will be collected and analyzed. With these samples,key microbial features will be determined for each well zone and,utilizing prior database information and modeling, used to createpredictive data for the oil-water contact levels in a well. Thispredictive or derived data will be used to drive production methods anddecisions.

Example 32

Accurate analytics of subsurface features is typically usefulinformation to the process of Enhanced Oil Recovery. Microbial EnhancedOil Recovery (MEOR) is a biological based technology consisting inmanipulating function or structure, or both, of microbial environmentsexisting in oil reservoirs. The ultimate aim of MEOR is to improve therecovery of oil entrapped in porous media while increasing economicprofits. MEOR is a tertiary oil extraction technology allowing thepartial recovery of the commonly residual two-thirds of oil, thusincreasing the life of mature oil reservoirs. The optimal application ofMEOR relies on having accurate subsurface analytic details on reservoirtemperature, pressure, depth, net pay, permeability, residual oil andwater saturations, porosity and fluid properties such as oil API gravityand viscosity.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples, flowback, and/or produced fluids(including but not limited to: hydrocarbons) during the drilling of asubsurface reservoir will be collected and analyzed. With these samples,key microbial features will be determined for each well zone and:utilizing prior database information and modeling, used to createpredictive data for the novel analytic analysis of a well. Thispredictive or derived data will be used to drive production methods anddecisions.

Example 33

Gas stations are under similar pressures to monitor and remediate anypotential environmental impacts. Because microbiomes are highlysensitive to environmental conditions they can act as an early indicatorof any environmental impacts.

Similarly to Example 16 and Example 17, samples extracted from soil andwater near gas stations will be collected and analyzed. With thesesamples, key microbial features will be determined for each gas stationand, utilizing prior database information and modeling, used to createpredictive data on the environmental impact of each gas station. Thispredictive or derived data will be used to drive station procedures andenvironmental remediation.

Exploration and Production of Hydrocarbons Industrial Use Examples:Microbial Measurements as a Predictive Tool for Key Parameters

Microbial communities acting as a predictive tool that can be used toquantify or qualify difficult or hard to predict parameters that areimportant to oil & gas production. These predictive tools can have oneor more of the following improvements relative to existing approaches:(a) be more cost effective, (d) provide greater accuracy or predictivepower, (c) allow for more data integration or analysis with existingwell logging tools or seismic data, and (d) any combination orvariations of the above.

Example 34

During the production of hydrocarbon, the oil/water interface in thereservoir subsurface will change over time. The production ratetypically has to be optimized such that maximum hydrocarbon can beextracted from the reservoir while minimizing the likelihood of oilcusping or coning. Oil cusping or coning is a condition where theunderlying water layer in a production zone enters the well bore due toan increased production rate. Oil cusping or coning can permanentlydamage the well bore and prevent the further extraction of hydrocarbon.Currently, predicting when oil cusping or coning occurs is verydifficult. Because microbiomes have unique properties based on theirsurrounding environment and levels of oil and water, they can serve asan early indicator or predictor of when oil cusping or coning may occur.With this early predictor, oil coning or cusping can be prevented.

Similarly to Example 16 and Example 17, samples extracted from coresamples, circulating mud, and/or produced fluids (including but notlimited to, hydrocarbons) will be collected and analyzed. With thesesamples, key microbial features will be determined for the well and,utilizing prior database information and modeling, used to createpredictive data on the likelihood of oil coning or cusping. Thispredictive or derived data will be used to determine the optimal rate ofproduction from a well head.

Example 35

Inter-well and intra-well informatics can be central to the evaluationof reservoir productivity and commercial valuation of new and existingoil leases. As outlined in Example 16, Example 17, microbiome sampleswill be collected during the extraction of oil and other fluids from newor existing wells. With these samples, key microbial features will bedetermined for each lease and, utilizing prior database information andmodeling, used to create predictive data on the features of potentialsurrounding oil patches. This predictive or derived data will be used todrive the commercial valuation of new leases or the commercial valuationof existing leases.

Example 36

The oil cuts and water cuts of produced oil can be a key factor whendetermining the value and method of production of a well. The cut of aparticular liquid is the ratio of the particular liquid producedcompared to the volume of total liquids produced. Produced liquids willcontain a water cut ratio ranging from 0-1. A crude oil can containwater, normally in the form of an emulsion. The emulsion should betreated inside heaters using chemicals, which will break the mixtureinto its individual components (water and crude oil). The processing ofthe water from crude oil adds time and expense to production.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples, flowback and/or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir will be collected and analyzed.With these samples, key microbial features will be determined for thesubsurface reservoir and, utilizing prior database information andmodeling, used to create predictive data for the oil and water cuts ofthe oil patch. This predictive or derived data will be used to driveproduction methods and decisions.

Example 37

The potential recovery factor of a reservoir typically can be a keyfactor when determining the value and method of production of a well.The recoverable amount of hydrocarbon initially in place, normallyexpressed as a percentage from 0-100%. The recovery factor is a functionof the displacement mechanism, subsurface geology, lithology, reservoirconnectivity, oil properties and several other chemical and physicalproperties of the reservoir. Enhanced oil recovery has emerged as ameans is to increase the recovery factor. Predicting the recovery factorand the potential effect of enhanced oil recovery methods during orprior to hydraulically fracturing a well will increase the efficiency ofan oil producer's operations.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples, flowback and/or produced hydrocarbonduring the drilling or production of a subsurface reservoir will becollected and analyzed. With these samples, key microbial features willbe determined for each well and, utilizing prior database informationand modeling, used to create predictive data for the recovery factor ofthe existing and potential future wells as well as the effectiveness ofany enhanced oil recovery techniques This predictive or derived datawill be used to drive production methods and decisions.

Example 38

The existence of hydrogen sulfide in a reservoir typically can be a keyfactor when determining the value and method of production of a well. Anextraordinarily poisonous gas with a molecular formula of H₂S. At lowconcentrations, H₂S has the odor of rotten eggs, but at higher, lethalconcentrations, it is odorless. H₂S is hazardous to workers and a fewseconds of exposure at relatively low concentrations can be lethal, butexposure to lower concentrations can also be harmful. The effect of H₂Sdepends on duration, frequency and intensity of exposure as well as thesusceptibility of the individual. Hydrogen sulfide is a serious andpotentially lethal hazard, so awareness, detection and monitoring of H₂Sis essential. Since hydrogen sulfide gas is present in some subsurfaceformations, drilling and other operational crews must be prepared to usedetection equipment, personal protective equipment, proper training andcontingency procedures in H₂S-prone areas. Hydrogen sulfide is producedduring the decomposition of organic matter and occurs with hydrocarbonsin some areas. It enters drilling mud from subsurface formations and canalso be generated by sulfate-reducing bacteria resident in thesubsurface. H₂S can cause sulfide-stress-corrosion cracking of metals.Because it is corrosive, H₂S production may require costly specialproduction equipment such as stainless steel tubing. H₂S production alsoreduces the value of the produced oil, as the amount of sulfur reducesthe value of oil from sweet (low sulfur content) to sour (high sulfurcontent). Because H₂S is often produced by bacteria in the reservoir,microbial analysis and predictive modeling provide a new avenue forearly detection of H₂S formation.

Similarly to Example 16 and Example 17, samples extracted from thecirculating mud, core samples, flowback, and/or produced fluids(including but not limited to, hydrocarbons) during the drilling orproduction of a subsurface reservoir will be collected and analyzed.With these samples, key microbial features will be determined for eachwell zone and, utilizing prior database information and modeling, usedto create predictive data for the existence of H₂S in existing andpotential future wells. This predictive or derived data will be used todrive production methods and decisions.

Example 39

The monitoring and prediction of leaky pipelines typically can be a keytechnique for increasing productivity and preventing environmentaldamage. While the detection of leaks is an important part of the oilproduction process, they do not prevent the formation of potentiallydamaging and costly leaks from initially occurring. Predicting andpreventing leaks prior to their formation is a more cost effective andenvironmentally conscious procedure. Current technology, however, makethe prediction of leaks difficult. Microbial analysis and predictivemodeling provide a new avenue for monitoring and predicting theformation of costly oil pipeline leaks.

Similarly to Example 16 and Example 17, samples extracted from the oil,fluids, and/or biofilm samples from each pipeline will be collected andanalyzed. With these samples, key microbial features will be determinedfor each pipeline and, utilizing prior database information andmodeling, used to create predictive data for the existence of current orfuture potential leaks the oil pipelines. This predictive or deriveddata will be used to drive production methods and decisions.

Example 40

The monitoring and prediction of the existing oil in a reservoirtypically can be a central technique for determining the value andmethod of production of a well. A central component to determining if areservoir is economically feasible to develop is to determine the oil inplace. The oil in place is the volume of oil in a reservoir prior toproduction. By combining information about the predicted oil in placewith other analytics, such as the predictive recovery factor and thecost of extraction, one can determine the economic feasibility ofrecovering the oil.

Similarly to Example 16 and Example 17, samples extracted from theproduced fluids (including but not limited to, hydrocarbons), coresamples, or circulating mud from each well will be collected andanalyzed. With these samples, key microbial features will be determinedfor each reservoir and, utilizing prior database information andmodeling, used to create predictive data for the oil in place ofexistence or future potential reservoirs. This predictive or deriveddata will be used to drive production methods and decisions.

Example 41

Turning to FIG. 17A there is shown a cross sectional view of an oilfield 1750, having a surface of the earth 1761 and having a borehole1762. The borehole 1762 extends between three intervals 1751, 1752,1753, e.g., zones, which in this embodiment correspond two threeformations, e.g., a first formation 1751, and a upper second formation1752 and a lower second formation 1753. The present evaluations areperformed on fluid samples, cutting and both from the borehole 1762.These evaluations provided a figure print of well. Thus turning to FIG.17B, there is shown a greatly simplified (for the purpose of clarity andillustration) finger print 1700 of the borehole 1762. The fingerprint1700 has rows corresponding to the three intervals, row 1701corresponding to interval 1751, row 1702 corresponding to interval 1752row 1703 corresponding to interval 1753. The columns 1710, 1711, 1712,to 1726 represent different taxa. And the abundance scale 1704, istypically a log rhythmic scale with increasing amounts of taxa in thedirection of the arrow. Thus, based upon the abundance and type of taxafound a fingerprint for the well, and intervals, can be determined. Thisfingerprint should typically be unique for every well.

It being recognized the the x-axis and y-axis can be interchanged, andthat these fingerprints, can be expressed in other like manner, such aspie charts, dot-matrix, bar graphs, scanner type barcodes (i.e.,manufacturing or consumer product type barcoding), and other graphic,human and machine readable manners of coding or presenting information.

About 48,600,000 DNA sequences were analyzed from samples taken frommaterial flowing from a well an oil field. In these well there are threeintervals. This DNA analysis identified about 147,000 taxa present inborehole. Of these taxa about 92% had never been identified before andwere not found in any known databases. This information was thenevaluated by the techniques of the present inventions and identified 152taxa of pertinence, or interest. From these 152 a fingerprint 1970 wasgenerated, and a photograph of that fingerprint 1790 is shown in FIG.17C.

It should be understood that the use of headings in this specificationis for the purpose of clarity, and is not limiting in any way. Thus, theprocesses and disclosures described under a heading should be read incontext with the entirely of this specification; including the variousexamples. The use of headings in this specification should not limit thescope of protection afford the present inventions. Thus, it should beunderstood that the teachings for one processes or apparatus, under oneheading, and the teachings for the other processes or apparatus, underother headings, can be applicable to each other, as well as, beingapplicable to other sections and teachings in this specification, andvice versa.

The various embodiments of applications; methods, activities andoperations set forth in this specification may be used for various otherfields and for various other activities, uses and embodiments.Additionally, these embodiments, for example, may be used with: existingsystems, articles, components, operations or activities; may be usedwith systems; articles, components, operations or activities that may bedeveloped in the future; and with such systems, articles, components,operations or activities that may be modified, in-part, based on theteachings of this specification. Further, the various embodiments andexamples set forth in this specification may be used with each other, inwhole or in part, and in different and various combinations. Thus, forexample, the configurations provided in the various embodiments andexamples of this specification may be used with each other; and thescope of protection afforded the present inventions should not belimited to a particular embodiment, example, configuration orarrangement that is set forth in a particular embodiment, example, or inan embodiment in a particular Figure.

The inventions may be embodied in other forms than those specificallydisclosed herein without departing from its spirit or essentialcharacteristics. The described embodiments are to be considered in allrespects only as illustrative and not restrictive.

What is claimed:
 1. A method comprising: accessing, using one or morecomputer processors, sequencing data from each of a plurality of samplessourced from an oil field, the sequencing data being stored in one ormore databases; accessing, using the one or more computer processors,industrial setting information corresponding to each of the plurality ofsamples, the industrial setting information comprising at least one ofGPS data, location data, true vertical well depth, measured well depth,a geological parameter, formation permeability, viscosity, porosity,pressure, flow, or temperature, the industrial setting information beingstored as metadata in the one or more databases; computationallydistilling, using the one or more computer processors, a large data setcomprising the metadata and microbiome information corresponding to thesequencing data, the large data set representing relationships betweenthe microbiome information and the industrial setting information in aconstruct having more than three dimensions, the computationaldistilling comprising using one or more transformation functions totransform the construct having the more than three dimensions into a setof two-dimensional or three-dimensional representations representing therelationships between the microbiome information and the industrialsetting information, the one or more transformation functions based onmachine-learned subsets of features in the microbiome information thatare predictive of the industrial setting information; and causing, usingthe one or more computer processors, an interactive visualization to bepresented on a client device, the interactive visualization comprisingelements for changing visual characteristics associated with one or moredata points of the set of the two-dimensional or three-dimensionalrepresentations to detect of associations between the microbiomeinformation and the industrial setting information.
 2. The method ofclaim 1, wherein, the microbiome information is selected from the groupconsisting of historic microbiome information, realtime microbiomeinformation derived microbiome information, and predictive microbiomeinformation.
 3. The method of claim 1, wherein the microbiomeinformation is based upon genetic material selected from the groupconsisting of a SSU rRNA gene 16S, SSU rRNA gene 18S, LSU rRNA gene 23S,LSU rRNA 28S, ITS in the rRNA operon, and ITS in the rRNA cpn60.
 4. Themethod of claim 3, wherein the microbiome information defines abiogeographical pattern.
 5. The method of claim 3, wherein themicrobiome information comprises information obtained from variableregions of the 16S rRNA.
 6. The method of claim 5, wherein the variableregions are selected from the group consisting of V2, V4, and V6.
 7. Themethod of claim 6, wherein the construct is represented as ann-dimensional plot, where n is selected from the group of integersconsisting of 4, 5, 6, 8, 9, 10, 11, 12, 13, and
 14. 8. The method ofclaim 1, wherein the statistical analysis further comprises determininga related nature of genetic material corresponding to the sequencingdata by measuring a change in gene sequences and using the measuredchange as a molecular clock.
 9. The method of claim 1, wherein thestatistical analysis further comprises determining a related nature ofgenetic material corresponding to the sequencing data by measuring achange selected from the group consisting of a change in gene sequences,and change in gene sequences and using the measured change as amolecular clock.
 10. The method of claim 1, further comprising causingdirecting information on a client device, the directing informationpertaining to directing recovery of a material from a borehole, whereinthe directing information comprises well wettability data.
 11. Themethod of claim 10, wherein the directing information comprisesproduction zone data related to improving vertical and aerialconformance, the production zone data comprising produced fluids dataand completion and production data.
 12. The method of claim 10, whereinthe directing information comprises a high resolution subsurfacegeologic map and logging information, the logging information comprisingat least one of gamma ray, triple combo, bit mechanics derived lithologyindicators, TOC and special core analyses information.
 13. The method ofclaim 10, wherein the directing information leads to, supports, or formsa basis for determining pay zones in the oil field.
 14. The method ofclaim 1, wherein the the client device is in a mobile vehicle at alocation within the oil field.
 15. The method of claim 1, wherein theoperational purposes comprise improving production in a waterflood orCO2 flood.
 16. The method of claim 1, wherein the operational purposescomprise informing reservoir connectivity or subsurface flow as anin-situ tracer.
 17. The method of claim 1, wherein the operationalpurposes comprise informing movement of produced water in thesubsurface.
 18. The method of claim 1, wherein the industrial settinginformation comprises three or more of GPS data, location data, truevertical well depth, measured well depth, a geological parameter,formation permeability, viscosity, porosity, pressure, flow, ortemperature.
 19. The method of claim 1, wherein the large data set is socharacterized by a time required for performing at least one type ofclustering exceeding a threshold time.
 20. The method of claim 19,wherein the threshold number of reads is 10 million reads.
 21. Themethod of claim 1, wherein the large data set is so characterized by anumber of reads exceeding a threshold number of reads.
 22. The method ofclaim 1, wherein the computational distilling further comprises:clustering the sequencing data into clusters; selecting representativesequences corresponding to each of the clusters; and using therepresentative sequences to reduce a complexity of the large data set.23. A system comprising: one or more computer processors; one or morecomputer memories; one or more instructions incorporated into the one ormore computer memories, the one or more instructions configuring the oneor more computer processors to perform operations comprising: accessing,using one or more computer processors, sequencing data from each of aplurality of samples sourced from an oil field, the sequencing databeing stored in one or more databases; accessing, using the one or morecomputer processors, industrial setting information corresponding toeach of the plurality of samples, the industrial setting informationcomprising at least one of GPS data, location data, true vertical welldepth, measured well depth, a geological parameter, formationpermeability, viscosity, porosity, pressure, flow, or temperature, theindustrial setting information being stored as metadata in the one ormore databases; computationally distilling, using the one or morecomputer processors, a large data set comprising the metadata andmicrobiome information corresponding to the sequencing data, the largedata set representing relationships between the microbiome informationand the industrial setting information in a construct having more thanthree dimensions, the computational distilling comprising using one ormore machine-learned transformation functions to transform the constructhaving more than three dimensions into a set of two-dimensional orthree-dimensional representations representing the relationships betweenthe microbiome information and the industrial setting information, theone or more transformation functions based on machine-learned subsets offeatures in the microbiome information that are predictive of theindustrial setting information; and causing, using the one or morecomputer processors, an interactive visualization to be presented on aclient device, the interactive visualization comprising elements forchanging visual characteristics associated with one or more data pointsof the set of the two-dimensional or three-dimensional representationsto detect of associations between the microbiome information and theindustrial setting information.
 24. The system of claim 23, wherein, themicrobiome information is selected from the group consisting of historicmicrobiome information, realtime microbiome information derivedmicrobiome information, and predictive microbiome information.
 25. Thesystem of claim 24, wherein the microbiome information comprisesinformation obtained from variable regions of the 16S rRNA.
 26. Thesystem of claim 25, wherein the variable regions are selected from thegroup consisting of V2, V4, and V6.
 27. The system of claim 23, whereinthe microbiome information is based upon genetic material selected fromthe group consisting of a SSU rRNA gene 16S, SSU rRNA gene 18S, LSU rRNAgene 23S, LSU rRNA 28S, ITS in the rRNA operon, and ITS in the rRNAcpn60.
 28. The system of claim 23, wherein the microbiome informationdefines a biogeographical pattern.
 29. The system of claim 23, whereinthe construct is represented as an n-dimensional plot, where n isselected from the group of integers consisting of 4, 5, 6, 8, 9, 10, 11,12, 13, and
 14. 30. The system of claim 23, wherein the statisticalanalysis further comprises determining a related nature of geneticmaterial corresponding to the sequencing data by measuring a change ingene sequences and using the measured change as a molecular clock. 31.The system of claim 23, wherein the statistical analysis furthercomprises determining a related nature of genetic material correspondingto the sequencing data by measuring a change selected from the groupconsisting of a change in gene sequences, and change in gene sequencesand using the measured change as a molecular clock.
 32. The system ofclaim 23, further comprising causing directing information on a clientdevice, the directing information pertaining to directing recovery of amaterial from a borehole, wherein the directing information compriseswell wettability data.
 33. The system of claim 32, wherein the directinginformation comprises production zone data related to improving verticaland aerial conformance, the production zone data comprising producedfluids data and completion and production data.
 34. The system of claim32, wherein the directing information comprises a high resolutionsubsurface geologic map and logging information, the logging informationcomprising at least one of gamma ray, triple combo, bit mechanicsderived lithology indicators, TOC and special core analyses information.35. The system of claim 32, wherein the directing information leads to,supports, or forms a basis for determining pay zones in the oil field.36. The system of claim 23, wherein the client device is in a mobilevehicle at a location within the oil field.
 37. The system of claim 23,wherein the operational purposes comprise improving production in awaterflood or CO2 flood.
 38. The system of claim 23, wherein theoperational purposes comprise informing reservoir connectivity orsubsurface flow as an in-situ tracer.
 39. The system of claim 23,wherein the operational purposes comprise informing movement of producedwater in the subsurface.
 40. The system of claim 23, wherein theindustrial setting information comprises three or more of GPS data,location data, true vertical well depth, measured well depth, ageological parameter, formation permeability, viscosity, porosity,pressure, flow, or temperature.
 41. A non-transitory machine-readablemedium storing a set of instructions, the set of instructions executableby one or more computer processors, the set of instructions configuringthe one or more computer processors to perform operations comprising:accessing sequencing data from each of a plurality of samples sourcedfrom an oil field, the sequencing data being stored in one or moredatabases; accessing industrial setting information corresponding toeach of the plurality of samples, the industrial setting informationcomprising at least one of GPS data, location data, true vertical welldepth, measured well depth, a geological parameter, formationpermeability, viscosity, porosity, pressure, flow, or temperature, theindustrial setting information being stored as metadata in the one ormore databases; computationally distilling a large data set comprisingthe metadata and microbiome information corresponding to the sequencingdata, the large data set representing relationships between themicrobiome information and the industrial setting information in aconstruct having more than three dimensions, the computationaldistilling comprising using one or more machine-learned transformationfunctions to transform the construct having more than three dimensionsinto a set of two-dimensional or three-dimensional representationsrepresenting the relationships between the microbiome information andthe industrial setting information, the one or more transformationfunctions based on machine-learned subsets of features in the microbiomeinformation that are predictive of the industrial setting information;and causing an interactive visualization to be presented on a clientdevice, the interactive visualization comprising elements for changingvisual characteristics associated with one or more data points of theset of the two-dimensional or three-dimensional representations todetect of associations between the microbiome information and theindustrial setting information.
 42. The non-transitory machine-readablemedium of claim 41, wherein, the microbiome information is selected fromthe group consisting of historic microbiome information, realtimemicrobiome information derived microbiome information, and predictivemicrobiome information.
 43. The non-transitory machine-readable mediumof claim 41, wherein the microbiome information is based upon geneticmaterial selected from the group consisting of a SSU rRNA gene 16S, SSUrRNA gene 18S, LSU rRNA gene 23S, LSU rRNA 28S, ITS in the rRNA operon,and ITS in the rRNA cpn60.
 44. The non-transitory machine-readablemedium of claim 43, wherein the microbiome information comprisesinformation obtained from variable regions of the 16S rRNA.
 45. Thenon-transitory machine-readable medium of claim 43, wherein the variableregions are selected from the group consisting of V2, V4, and V6. 46.The non-transitory machine-readable medium of claim 41, wherein themicrobiome information defines a biogeographical pattern.
 47. Thenon-transitory machine-readable medium of claim 41, wherein theconstruct is represented as an n-dimensional plot, where n is selectedfrom the group of integers consisting of 4, 5, 6, 8, 9, 10, 11, 12, 13,and
 14. 48. The non-transitory machine-readable medium of claim 41,wherein the statistical analysis further comprises determining a relatednature of genetic material corresponding to the sequencing data bymeasuring a change in gene sequences and using the measured change as amolecular clock.
 49. The non-transitory machine-readable medium of claim41, wherein the statistical analysis further comprises determining arelated nature of genetic material corresponding to the sequencing databy measuring a change selected from the group consisting of a change ingene sequences, and change in gene sequences and using the measuredchange as a molecular clock.
 50. The non-transitory machine-readablemedium of claim 41, further comprising causing directing information ona client device, the directing information pertaining to directingrecovery of a material from a borehole, wherein the directinginformation comprises well wettability data.
 51. The non-transitorymachine-readable medium of claim 50, wherein the directing informationcomprises production zone data related to improving vertical and aerialconformance, the production zone data comprising produced fluids dataand completion and production data.
 52. The non-transitorymachine-readable medium of claim 50, wherein the directing informationcomprises a high resolution subsurface geologic map and logginginformation, the logging information comprising at least one of gammaray, triple combo, bit mechanics derived lithology indicators, TOC andspecial core analyses information.
 53. The non-transitorymachine-readable medium of claim 50, wherein the directing informationleads to, supports, or forms a basis for determining pay zones in theoil field.
 54. The non-transitory machine-readable medium of claim 41,wherein the client device is in a mobile vehicle at a location withinthe oil field.
 55. The non-transitory machine-readable medium of claim41, wherein the operational purposes comprise improving production in awaterflood or CO2 flood.
 56. The non-transitory machine-readable mediumof claim 41, wherein the operational purposes comprise informingreservoir connectivity or subsurface flow as an in-situ tracer.
 57. Thenon-transitory machine-readable medium of claim 41, wherein theoperational purposes comprise informing movement of produced water inthe subsurface.
 58. The non-transitory machine-readable medium of claim41, wherein the industrial setting information comprises three or moreof GPS data, location data, true vertical well depth, measured welldepth, a geological parameter, formation permeability, viscosity,porosity, pressure, flow, or temperature.